Starting phenix.real_space_refine
on Fri Aug 22 17:07:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxu_40859/08_2025/8sxu_40859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxu_40859/08_2025/8sxu_40859.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2025/8sxu_40859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2025/8sxu_40859.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2025/8sxu_40859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2025/8sxu_40859.map"
  }
  resolution = 3.66
  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=   0.002 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      20      5.16       5
     C    3981      2.51       5
     N    1064      2.21       5
     O    1132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6207
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5987
          Classifications: {'peptide': 726}
          Link IDs: {'PTRANS': 33, 'TRANS': 692}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 220
          Classifications: {'RNA': 10}
          Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 5}
          Link IDs: {'rna2p': 4, 'rna3p': 5}
  Time building chain proxies: 1.37, per 1000 atoms: 0.22
  Number of scatterers: 6207
  At special positions: 0
  Unit cell: (82.6, 82.6, 101.598, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P      10     15.00
     O    1132      8.00
     N    1064      7.00
     C    3981      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: 0.41
  Conformation dependent library (CDL) restraints added in 344.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      58.8% alpha, 6.3% beta
      0 base pairs and 1 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 255 through 258
    Processing helix  chain 'A' and resid 259 through 275
      removed outlier: 4.127A  pdb=" N   PHE A 274 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 310
      removed outlier: 3.937A  pdb=" N   LEU A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 421
      removed outlier: 3.770A  pdb=" N   GLN A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   THR A 409 " --> pdb=" O   THR A 405 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASN A 421 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 436
      removed outlier: 3.796A  pdb=" N   THR A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   PHE A 432 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 433 " --> pdb=" O   MET A 429 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR A 436 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 450
    Processing helix  chain 'A' and resid 454 through 464
      removed outlier: 4.069A  pdb=" N   ILE A 458 " --> pdb=" O   THR A 454 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   VAL A 459 " --> pdb=" O   GLY A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 484
      removed outlier: 3.866A  pdb=" N   GLN A 482 " --> pdb=" O   ALA A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 503
      removed outlier: 3.727A  pdb=" N   LEU A 488 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
      Proline residue:  A 490  - end of helix
      removed outlier: 4.230A  pdb=" N   LEU A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE A 499 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS A 501 " --> pdb=" O   GLN A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 510
    Processing helix  chain 'A' and resid 526 through 528
      No H-bonds generated for 'chain 'A' and resid 526 through 528'
    Processing helix  chain 'A' and resid 537 through 553
      removed outlier: 3.542A  pdb=" N   LYS A 545 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 546 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A 547 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 572 through 589
      removed outlier: 4.321A  pdb=" N   ILE A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   VAL A 582 " --> pdb=" O   LYS A 578 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 620
    Processing helix  chain 'A' and resid 624 through 634
    Processing helix  chain 'A' and resid 662 through 682
      removed outlier: 4.550A  pdb=" N   LEU A 666 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE A 670 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 675 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 730
      removed outlier: 3.740A  pdb=" N   LEU A 721 " --> pdb=" O   ASN A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 757
      removed outlier: 3.875A  pdb=" N   GLN A 752 " --> pdb=" O   GLN A 748 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ILE A 753 " --> pdb=" O   THR A 749 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET A 754 " --> pdb=" O   GLU A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 778
      No H-bonds generated for 'chain 'A' and resid 776 through 778'
    Processing helix  chain 'A' and resid 779 through 796
      Proline residue:  A 787  - end of helix
      removed outlier: 3.675A  pdb=" N   ILE A 792 " --> pdb=" O   LEU A 788 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLU A 794 " --> pdb=" O   LYS A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 816
      removed outlier: 3.966A  pdb=" N   ILE A 810 " --> pdb=" O   TRP A 806 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASN A 811 " --> pdb=" O   VAL A 807 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ILE A 812 " --> pdb=" O   GLY A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 828
      removed outlier: 4.204A  pdb=" N   LYS A 820 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 822 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   TYR A 823 " --> pdb=" O   PRO A 819 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG A 824 " --> pdb=" O   LYS A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 849
      removed outlier: 3.885A  pdb=" N   PHE A 837 " --> pdb=" O   PRO A 833 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU A 839 " --> pdb=" O   THR A 835 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 840 " --> pdb=" O   PHE A 836 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TRP A 849 " --> pdb=" O   LEU A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 862
    Processing helix  chain 'A' and resid 874 through 886
      removed outlier: 3.778A  pdb=" N   THR A 886 " --> pdb=" O   THR A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 893
      removed outlier: 4.156A  pdb=" N   TRP A 890 " --> pdb=" O   THR A 886 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR A 891 " --> pdb=" O   ALA A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 902
    Processing helix  chain 'A' and resid 933 through 947
      removed outlier: 3.508A  pdb=" N   CYS A 944 " --> pdb=" O   TRP A 940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 966
    Processing helix  chain 'A' and resid 970 through 979
      removed outlier: 3.844A  pdb=" N   ILE A 974 " --> pdb=" O   LYS A 970 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 975 " --> pdb=" O   PRO A 971 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A 977 " --> pdb=" O   THR A 973 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU A 979 " --> pdb=" O   LYS A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 989
      removed outlier: 3.563A  pdb=" N   ILE A 988 " --> pdb=" O   THR A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1003
      removed outlier: 3.655A  pdb=" N   MET A1002 " --> pdb=" O   THR A 998 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A1003 " --> pdb=" O   PRO A 999 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 998 through 1003'
    Processing helix  chain 'A' and resid 1009 through 1018
      removed outlier: 3.575A  pdb=" N   ILE A1014 " --> pdb=" O   LYS A1010 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1030
      removed outlier: 3.905A  pdb=" N   VAL A1029 " --> pdb=" O   THR A1025 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1040
      removed outlier: 3.702A  pdb=" N   ILE A1039 " --> pdb=" O   THR A1035 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE A1040 " --> pdb=" O   TRP A1036 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1061
      removed outlier: 3.627A  pdb=" N   ARG A1052 " --> pdb=" O   GLY A1048 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 530 through 536
      removed outlier: 6.283A  pdb=" N   ALA A 512 " --> pdb=" O   ASN A 640 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ILE A 642 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ILE A 514 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA A 639 " --> pdb=" O   ALA A 650 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ALA A 650 " --> pdb=" O   ALA A 639 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ILE A 641 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 643 " --> pdb=" O   GLN A 646 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 697 through 698
      removed outlier: 4.066A  pdb=" N   GLN A 739 " --> pdb=" O   SER A 598 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 688 through 690
    Processing sheet with id=AA4, first strand: chain 'A' and resid 767 through 768

    244 hydrogen bonds defined for protein.
    705 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      1 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1920
        1.34 -     1.46: 1360
        1.46 -     1.58: 3033
        1.58 -     1.69: 20
        1.69 -     1.81: 34
  Bond restraints: 6367
  Sorted by residual:
  bond pdb=" CB  PRO A 471 "
       pdb=" CG  PRO A 471 "
    ideal  model  delta    sigma   weight residual
    1.492  1.591 -0.099 5.00e-02 4.00e+02 3.94e+00
  bond pdb=" CB  PRO A 652 "
       pdb=" CG  PRO A 652 "
    ideal  model  delta    sigma   weight residual
    1.492  1.556 -0.064 5.00e-02 4.00e+02 1.66e+00
  bond pdb=" C   VAL A 695 "
       pdb=" N   LYS A 696 "
    ideal  model  delta    sigma   weight residual
    1.332  1.318  0.015 1.40e-02 5.10e+03 1.11e+00
  bond pdb=" CG  PRO A 471 "
       pdb=" CD  PRO A 471 "
    ideal  model  delta    sigma   weight residual
    1.503  1.534 -0.031 3.40e-02 8.65e+02 8.25e-01
  bond pdb=" CB  MET A 834 "
       pdb=" CG  MET A 834 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.72e-01
  ... (remaining 6362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 8537
        2.13 -     4.27: 85
        4.27 -     6.40: 16
        6.40 -     8.53: 4
        8.53 -    10.67: 1
  Bond angle restraints: 8643
  Sorted by residual:
  angle pdb=" CB  MET A 834 "
        pdb=" CG  MET A 834 "
        pdb=" SD  MET A 834 "
      ideal   model   delta    sigma   weight residual
     112.70  123.37  -10.67 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" CA  MET A 908 "
        pdb=" CB  MET A 908 "
        pdb=" CG  MET A 908 "
      ideal   model   delta    sigma   weight residual
     114.10  120.89   -6.79 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" N   VAL A 564 "
        pdb=" CA  VAL A 564 "
        pdb=" C   VAL A 564 "
      ideal   model   delta    sigma   weight residual
     113.10  109.89    3.21 9.70e-01 1.06e+00 1.09e+01
  angle pdb=" CA  PRO A 471 "
        pdb=" N   PRO A 471 "
        pdb=" CD  PRO A 471 "
      ideal   model   delta    sigma   weight residual
     112.00  107.84    4.16 1.40e+00 5.10e-01 8.84e+00
  angle pdb=" CA  MET A 834 "
        pdb=" CB  MET A 834 "
        pdb=" CG  MET A 834 "
      ideal   model   delta    sigma   weight residual
     114.10  119.55   -5.45 2.00e+00 2.50e-01 7.43e+00
  ... (remaining 8638 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.16: 3487
       25.16 -    50.31: 329
       50.31 -    75.47: 41
       75.47 -   100.62: 12
      100.62 -   125.78: 1
  Dihedral angle restraints: 3870
    sinusoidal: 1722
      harmonic: 2148
  Sorted by residual:
  dihedral pdb=" O4'   A C  11 "
           pdb=" C1'   A C  11 "
           pdb=" N9    A C  11 "
           pdb=" C4    A C  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  154.63  -86.63     1      1.70e+01 3.46e-03 3.13e+01
  dihedral pdb=" O4'   A C   9 "
           pdb=" C1'   A C   9 "
           pdb=" N9    A C   9 "
           pdb=" C4    A C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  130.20  -62.20     1      1.70e+01 3.46e-03 1.77e+01
  dihedral pdb=" CA  MET A 908 "
           pdb=" C   MET A 908 "
           pdb=" N   PRO A 909 "
           pdb=" CA  PRO A 909 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.43  -20.57     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 3867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 569
       0.028 -    0.056: 272
       0.056 -    0.084: 74
       0.084 -    0.111: 43
       0.111 -    0.139: 8
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" CA  PRO A 909 "
            pdb=" N   PRO A 909 "
            pdb=" C   PRO A 909 "
            pdb=" CB  PRO A 909 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  ILE A 802 "
            pdb=" N   ILE A 802 "
            pdb=" C   ILE A 802 "
            pdb=" CB  ILE A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  ILE A 830 "
            pdb=" N   ILE A 830 "
            pdb=" C   ILE A 830 "
            pdb=" CB  ILE A 830 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  ... (remaining 963 not shown)

  Planarity restraints: 1042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 288 "    0.017 2.00e-02 2.50e+03   1.39e-02 4.82e+00
        pdb=" CG  TRP A 288 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 288 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 288 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 288 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 288 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 288 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 288 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 288 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 288 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 954 "    0.035 5.00e-02 4.00e+02   5.30e-02 4.50e+00
        pdb=" N   PRO A 955 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 955 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 955 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 470 "   -0.034 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO A 471 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 471 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 471 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1039 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 386
        2.73 -     3.27: 6798
        3.27 -     3.81: 10803
        3.81 -     4.36: 12577
        4.36 -     4.90: 20186
  Nonbonded interactions: 50750
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 534 "
            pdb=" O   GLN A 659 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   LYS A1017 "
            pdb=" OG1 THR A1021 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   TRP A 899 "
            pdb=" OG1 THR A 902 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   CYS A 661 "
            pdb=" OG  SER A 664 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   THR A 954 "
            pdb=" OG1 THR A 957 "
     model   vdw
     2.230 3.040
  ... (remaining 50745 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.900
  Find NCS groups from input model:        0.020
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6592
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      :  0.003   0.099   6367  Z= 0.108
  Angle     :  0.571  10.665   8643  Z= 0.291
  Chirality :  0.039   0.139    966
  Planarity :  0.004   0.053   1042
  Dihedral  : 18.376 125.781   2474
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 31.07 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.09 (0.33), residues: 722
  helix:  0.61 (0.31), residues: 306
  sheet: -0.42 (0.90), residues: 43
  loop : -0.51 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 577 
 TYR   0.005   0.001   TYR A 912 
 PHE   0.020   0.001   PHE A 651 
 TRP   0.037   0.002   TRP A 288 
 HIS   0.002   0.001   HIS A 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6367)
  covalent geometry    : angle       0.57072 ( 8643)
  hydrogen bonds       : bond        0.28648 (  244)
  hydrogen bonds       : angle       8.20326 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 MET cc_start: 0.3185 (mmt) cc_final: 0.2804 (mmt)
REVERT: A  288 TRP cc_start: 0.7789 (t-100) cc_final: 0.7512 (t-100)
REVERT: A  505 LEU cc_start: 0.7792 (mp) cc_final: 0.7453 (mp)
REVERT: A  536 MET cc_start: 0.6887 (ptp) cc_final: 0.6429 (ptp)
REVERT: A  538 ILE cc_start: 0.7835 (mm) cc_final: 0.7608 (mp)
REVERT: A  542 ILE cc_start: 0.8443 (mt) cc_final: 0.8164 (mt)
REVERT: A  560 HIS cc_start: 0.7150 (t-90) cc_final: 0.6456 (t-90)
REVERT: A  573 TRP cc_start: 0.7753 (p-90) cc_final: 0.7502 (p-90)
REVERT: A  627 LEU cc_start: 0.6972 (mt) cc_final: 0.6553 (mt)
REVERT: A  654 LYS cc_start: 0.7311 (mmtp) cc_final: 0.6892 (mmtm)
REVERT: A  666 LEU cc_start: 0.8573 (mm) cc_final: 0.8330 (mm)
REVERT: A  673 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6859 (tm-30)
REVERT: A  680 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.8442 (mtm-85)
REVERT: A  710 ASN cc_start: 0.7593 (t0) cc_final: 0.7241 (p0)
REVERT: A  746 ASN cc_start: 0.7794 (t0) cc_final: 0.7570 (t0)
REVERT: A  759 PHE cc_start: 0.7536 (m-80) cc_final: 0.7024 (m-80)
REVERT: A  764 LYS cc_start: 0.6870 (tmmt) cc_final: 0.6668 (tmtt)
REVERT: A  766 ILE cc_start: 0.7469 (pt) cc_final: 0.6725 (pt)
REVERT: A  772 GLN cc_start: 0.6497 (mm-40) cc_final: 0.6252 (mm110)
REVERT: A  791 GLU cc_start: 0.8402 (tp30) cc_final: 0.8090 (tp30)
REVERT: A  815 MET cc_start: 0.5936 (tmm) cc_final: 0.5234 (tmm)
REVERT: A  823 TYR cc_start: 0.8196 (t80) cc_final: 0.7947 (t80)
REVERT: A  876 LYS cc_start: 0.7527 (tptt) cc_final: 0.7320 (tptt)
REVERT: A  883 VAL cc_start: 0.8772 (t) cc_final: 0.8538 (t)
REVERT: A  919 LYS cc_start: 0.7805 (tmtt) cc_final: 0.7560 (ttpt)
REVERT: A  986 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8036 (pp30)
REVERT: A  997 LYS cc_start: 0.7507 (ttmm) cc_final: 0.7255 (mtmt)
REVERT: A 1055 ASN cc_start: 0.7381 (t0) cc_final: 0.6801 (t0)
REVERT: A 1059 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8040 (mm-40)
  outliers start: 1
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0911
  time to fit residues: 20.1114
Evaluate side-chains
  147 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0000
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 752 GLN
A 826 ASN
A 851 GLN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.164823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.136993 restraints weight = 11683.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.141751 restraints weight = 6653.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.145321 restraints weight = 4436.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.147692 restraints weight = 3254.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.148694 restraints weight = 2593.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
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      :  0.003   0.057   6367  Z= 0.149
  Angle     :  0.636   7.459   8643  Z= 0.328
  Chirality :  0.042   0.159    966
  Planarity :  0.005   0.054   1042
  Dihedral  :  9.991 120.334    898
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 26.55 %
    Favored  : 68.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.35 (0.33), residues: 722
  helix:  0.19 (0.27), residues: 357
  sheet: -1.03 (0.84), residues: 43
  loop : -0.45 (0.39), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 412 
 TYR   0.010   0.001   TYR A1054 
 PHE   0.014   0.001   PHE A 781 
 TRP   0.031   0.002   TRP A 288 
 HIS   0.003   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6367)
  covalent geometry    : angle       0.63640 ( 8643)
  hydrogen bonds       : bond        0.05149 (  244)
  hydrogen bonds       : angle       5.76605 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7897 (p)
REVERT: A  536 MET cc_start: 0.7215 (ptp) cc_final: 0.6874 (ptp)
REVERT: A  538 ILE cc_start: 0.7951 (mm) cc_final: 0.7653 (mp)
REVERT: A  539 ASP cc_start: 0.7980 (p0) cc_final: 0.7429 (p0)
REVERT: A  542 ILE cc_start: 0.8517 (mt) cc_final: 0.8310 (mt)
REVERT: A  547 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7643 (mt)
REVERT: A  552 GLN cc_start: 0.7308 (tp-100) cc_final: 0.6949 (mt0)
REVERT: A  560 HIS cc_start: 0.7106 (t-90) cc_final: 0.6867 (t-90)
REVERT: A  578 LYS cc_start: 0.7781 (tttp) cc_final: 0.7339 (tttp)
REVERT: A  627 LEU cc_start: 0.7372 (mt) cc_final: 0.7030 (mt)
REVERT: A  651 PHE cc_start: 0.7412 (p90) cc_final: 0.6674 (p90)
REVERT: A  654 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7625 (mptt)
REVERT: A  666 LEU cc_start: 0.8726 (mm) cc_final: 0.8472 (mm)
REVERT: A  673 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6420 (tm-30)
REVERT: A  710 ASN cc_start: 0.8049 (t0) cc_final: 0.7626 (p0)
REVERT: A  759 PHE cc_start: 0.7200 (m-80) cc_final: 0.6476 (m-80)
REVERT: A  766 ILE cc_start: 0.7638 (pt) cc_final: 0.7309 (pt)
REVERT: A  772 GLN cc_start: 0.6702 (mm-40) cc_final: 0.6409 (mm-40)
REVERT: A  789 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7024 (pp)
REVERT: A  790 LYS cc_start: 0.8612 (ptpp) cc_final: 0.7839 (ptpp)
REVERT: A  793 LYS cc_start: 0.8941 (mttt) cc_final: 0.8389 (mttt)
REVERT: A  815 MET cc_start: 0.5410 (tmm) cc_final: 0.4613 (tmm)
REVERT: A  823 TYR cc_start: 0.7766 (t80) cc_final: 0.7492 (t80)
REVERT: A  834 MET cc_start: 0.6904 (tmm) cc_final: 0.6599 (tmm)
REVERT: A  837 PHE cc_start: 0.7762 (m-80) cc_final: 0.7503 (m-80)
REVERT: A  876 LYS cc_start: 0.7699 (tptt) cc_final: 0.7410 (tptt)
REVERT: A  919 LYS cc_start: 0.8492 (tmtt) cc_final: 0.8123 (ttpt)
REVERT: A  939 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6502 (m-40)
REVERT: A 1002 MET cc_start: 0.6585 (mmm) cc_final: 0.6380 (mmm)
REVERT: A 1017 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6980 (ptpp)
REVERT: A 1058 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8086 (ttmm)
  outliers start: 36
  outliers final: 20
  residues processed: 189
  average time/residue: 0.0748
  time to fit residues: 18.3586
Evaluate side-chains
  171 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  675 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1031 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   chunk 13 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN
** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.161439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.134977 restraints weight = 11500.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.139735 restraints weight = 6555.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.143052 restraints weight = 4307.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.145412 restraints weight = 3132.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.147159 restraints weight = 2460.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6470
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6367  Z= 0.135
  Angle     :  0.625   8.352   8643  Z= 0.322
  Chirality :  0.042   0.162    966
  Planarity :  0.004   0.051   1042
  Dihedral  :  9.915 116.017    898
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 27.30 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.48 (0.32), residues: 722
  helix:  0.20 (0.28), residues: 352
  sheet: -1.19 (0.82), residues: 43
  loop : -0.66 (0.38), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 747 
 TYR   0.009   0.001   TYR A1054 
 PHE   0.015   0.001   PHE A 781 
 TRP   0.020   0.002   TRP A 288 
 HIS   0.009   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6367)
  covalent geometry    : angle       0.62498 ( 8643)
  hydrogen bonds       : bond        0.04521 (  244)
  hydrogen bonds       : angle       5.44468 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 171
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.8415 (mttp) cc_final: 0.8194 (mttp)
REVERT: A  405 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7919 (p)
REVERT: A  428 GLU cc_start: 0.6710 (mp0) cc_final: 0.6475 (mp0)
REVERT: A  491 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8293 (m-80)
REVERT: A  531 ARG cc_start: 0.3536 (mmt180) cc_final: 0.2791 (tpt170)
REVERT: A  536 MET cc_start: 0.7222 (ptp) cc_final: 0.6914 (ptp)
REVERT: A  538 ILE cc_start: 0.8013 (mm) cc_final: 0.7671 (mp)
REVERT: A  542 ILE cc_start: 0.8496 (mt) cc_final: 0.8273 (mt)
REVERT: A  545 LYS cc_start: 0.8526 (tttt) cc_final: 0.8229 (mttt)
REVERT: A  560 HIS cc_start: 0.7151 (t-90) cc_final: 0.6847 (t-90)
REVERT: A  597 ILE cc_start: 0.7739 (mp) cc_final: 0.7254 (mm)
REVERT: A  607 LYS cc_start: 0.7430 (pttm) cc_final: 0.7217 (ttpt)
REVERT: A  651 PHE cc_start: 0.7451 (p90) cc_final: 0.6753 (p90)
REVERT: A  654 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7603 (mptt)
REVERT: A  666 LEU cc_start: 0.8738 (mm) cc_final: 0.8477 (mm)
REVERT: A  673 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6511 (tm-30)
REVERT: A  710 ASN cc_start: 0.7997 (t0) cc_final: 0.7597 (p0)
REVERT: A  766 ILE cc_start: 0.7574 (pt) cc_final: 0.7259 (pt)
REVERT: A  772 GLN cc_start: 0.6871 (mm-40) cc_final: 0.6581 (mm-40)
REVERT: A  789 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7068 (pp)
REVERT: A  790 LYS cc_start: 0.8589 (ptpp) cc_final: 0.7879 (ptpp)
REVERT: A  793 LYS cc_start: 0.8943 (mttt) cc_final: 0.8400 (mttt)
REVERT: A  815 MET cc_start: 0.5412 (tmm) cc_final: 0.4610 (tmm)
REVERT: A  820 LYS cc_start: 0.8236 (tptt) cc_final: 0.8036 (tptt)
REVERT: A  823 TYR cc_start: 0.7870 (t80) cc_final: 0.7548 (t80)
REVERT: A  834 MET cc_start: 0.6913 (tmm) cc_final: 0.6521 (tmm)
REVERT: A  876 LYS cc_start: 0.7768 (tptt) cc_final: 0.7563 (tptt)
REVERT: A  880 LYS cc_start: 0.7542 (ttmm) cc_final: 0.7141 (mmtt)
REVERT: A  939 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.6128 (t0)
REVERT: A 1002 MET cc_start: 0.6515 (mmm) cc_final: 0.6250 (mmm)
  outliers start: 35
  outliers final: 21
  residues processed: 193
  average time/residue: 0.0834
  time to fit residues: 20.4916
Evaluate side-chains
  190 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1031 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 66 optimal weight:    0.0060
   chunk 14 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0770
   chunk 49 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0060
   chunk 52 optimal weight:   40.0000
   chunk 6 optimal weight:    8.9990
   overall best weight:    0.3370

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.164234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.137924 restraints weight = 11502.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.142718 restraints weight = 6495.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.146173 restraints weight = 4225.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.148295 restraints weight = 3025.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.150074 restraints weight = 2381.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6367  Z= 0.117
  Angle     :  0.605   6.878   8643  Z= 0.307
  Chirality :  0.041   0.156    966
  Planarity :  0.004   0.055   1042
  Dihedral  :  9.718 109.840    898
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 28.05 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.34 (0.33), residues: 722
  helix:  0.33 (0.28), residues: 346
  sheet: -1.20 (0.81), residues: 43
  loop : -0.57 (0.38), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 747 
 TYR   0.022   0.001   TYR A 414 
 PHE   0.014   0.001   PHE A 781 
 TRP   0.025   0.002   TRP A 288 
 HIS   0.008   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6367)
  covalent geometry    : angle       0.60463 ( 8643)
  hydrogen bonds       : bond        0.03933 (  244)
  hydrogen bonds       : angle       5.18345 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLU cc_start: 0.6668 (mp0) cc_final: 0.6425 (mp0)
REVERT: A  479 GLU cc_start: 0.7065 (tp30) cc_final: 0.6589 (tp30)
REVERT: A  491 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (m-80)
REVERT: A  531 ARG cc_start: 0.3602 (mmt180) cc_final: 0.2681 (tpt170)
REVERT: A  536 MET cc_start: 0.7210 (ptp) cc_final: 0.6912 (ptp)
REVERT: A  538 ILE cc_start: 0.7955 (mm) cc_final: 0.7635 (mp)
REVERT: A  539 ASP cc_start: 0.7961 (p0) cc_final: 0.7573 (p0)
REVERT: A  542 ILE cc_start: 0.8491 (mt) cc_final: 0.8270 (mt)
REVERT: A  545 LYS cc_start: 0.8462 (tttt) cc_final: 0.8157 (mttt)
REVERT: A  578 LYS cc_start: 0.7774 (tttm) cc_final: 0.7285 (tttp)
REVERT: A  597 ILE cc_start: 0.7709 (mp) cc_final: 0.7296 (mm)
REVERT: A  617 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5851 (tp)
REVERT: A  640 ASN cc_start: 0.7676 (p0) cc_final: 0.7251 (p0)
REVERT: A  651 PHE cc_start: 0.7355 (p90) cc_final: 0.6730 (p90)
REVERT: A  654 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7660 (mptt)
REVERT: A  666 LEU cc_start: 0.8657 (mm) cc_final: 0.8384 (mm)
REVERT: A  673 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6657 (tm-30)
REVERT: A  766 ILE cc_start: 0.7609 (pt) cc_final: 0.7310 (pt)
REVERT: A  772 GLN cc_start: 0.6869 (mm-40) cc_final: 0.6595 (mm-40)
REVERT: A  789 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7010 (pp)
REVERT: A  790 LYS cc_start: 0.8518 (ptpp) cc_final: 0.7851 (ptpp)
REVERT: A  793 LYS cc_start: 0.8926 (mttt) cc_final: 0.8392 (mttt)
REVERT: A  815 MET cc_start: 0.5353 (tmm) cc_final: 0.4531 (tmm)
REVERT: A  820 LYS cc_start: 0.8261 (tptt) cc_final: 0.7591 (tptt)
REVERT: A  823 TYR cc_start: 0.7883 (t80) cc_final: 0.7497 (t80)
REVERT: A  834 MET cc_start: 0.6800 (tmm) cc_final: 0.6382 (tmm)
REVERT: A  876 LYS cc_start: 0.7757 (tptt) cc_final: 0.7529 (tptt)
REVERT: A  880 LYS cc_start: 0.7469 (ttmm) cc_final: 0.7137 (mmtt)
REVERT: A  939 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.6474 (t0)
REVERT: A  949 LEU cc_start: 0.7377 (tt) cc_final: 0.6417 (mt)
REVERT: A  997 LYS cc_start: 0.8304 (tmtt) cc_final: 0.7625 (mmtt)
REVERT: A 1002 MET cc_start: 0.6484 (mmm) cc_final: 0.6205 (mmm)
REVERT: A 1058 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7796 (ttmm)
  outliers start: 36
  outliers final: 22
  residues processed: 193
  average time/residue: 0.0956
  time to fit residues: 23.3027
Evaluate side-chains
  185 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  675 LEU
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0970
   chunk 9 optimal weight:    0.2980
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
A 900 ASN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.161987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.134929 restraints weight = 11745.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.139845 restraints weight = 6485.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.143400 restraints weight = 4179.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.145719 restraints weight = 2969.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.146970 restraints weight = 2311.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6367  Z= 0.153
  Angle     :  0.647   7.197   8643  Z= 0.331
  Chirality :  0.043   0.152    966
  Planarity :  0.005   0.051   1042
  Dihedral  :  9.579 101.358    898
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 27.90 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.43 (0.33), residues: 722
  helix:  0.17 (0.28), residues: 352
  sheet: -1.33 (0.78), residues: 43
  loop : -0.49 (0.38), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 747 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.019   0.002   TRP A 288 
 HIS   0.009   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6367)
  covalent geometry    : angle       0.64663 ( 8643)
  hydrogen bonds       : bond        0.04012 (  244)
  hydrogen bonds       : angle       5.13211 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLU cc_start: 0.6905 (mp0) cc_final: 0.6648 (mp0)
REVERT: A  463 ASN cc_start: 0.8080 (m-40) cc_final: 0.7832 (m110)
REVERT: A  479 GLU cc_start: 0.7045 (tp30) cc_final: 0.6742 (tp30)
REVERT: A  491 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8272 (m-80)
REVERT: A  531 ARG cc_start: 0.3217 (mmt180) cc_final: 0.2507 (tpt170)
REVERT: A  536 MET cc_start: 0.7272 (ptp) cc_final: 0.6923 (ptp)
REVERT: A  539 ASP cc_start: 0.8063 (p0) cc_final: 0.7680 (p0)
REVERT: A  545 LYS cc_start: 0.8480 (tttt) cc_final: 0.8117 (mtpt)
REVERT: A  597 ILE cc_start: 0.7609 (mp) cc_final: 0.7176 (mm)
REVERT: A  607 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7215 (tppt)
REVERT: A  617 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5725 (tp)
REVERT: A  651 PHE cc_start: 0.7465 (p90) cc_final: 0.6875 (p90)
REVERT: A  654 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7603 (mptt)
REVERT: A  666 LEU cc_start: 0.8744 (mm) cc_final: 0.8533 (mm)
REVERT: A  672 LEU cc_start: 0.8358 (mm) cc_final: 0.7951 (mm)
REVERT: A  673 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6653 (tm-30)
REVERT: A  742 LEU cc_start: 0.8426 (tp) cc_final: 0.8140 (mp)
REVERT: A  789 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7249 (pp)
REVERT: A  790 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8154 (ptpp)
REVERT: A  793 LYS cc_start: 0.8981 (mttt) cc_final: 0.8430 (mttt)
REVERT: A  815 MET cc_start: 0.5518 (tmm) cc_final: 0.4683 (tmm)
REVERT: A  820 LYS cc_start: 0.8383 (tptt) cc_final: 0.7701 (tptt)
REVERT: A  823 TYR cc_start: 0.8042 (t80) cc_final: 0.7670 (t80)
REVERT: A  834 MET cc_start: 0.6908 (tmm) cc_final: 0.6395 (tmm)
REVERT: A  837 PHE cc_start: 0.7800 (m-80) cc_final: 0.6989 (m-80)
REVERT: A  876 LYS cc_start: 0.7852 (tptt) cc_final: 0.7627 (tptt)
REVERT: A  932 LEU cc_start: 0.2124 (OUTLIER) cc_final: 0.0528 (mt)
REVERT: A  939 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6248 (t0)
REVERT: A  997 LYS cc_start: 0.8332 (tmtt) cc_final: 0.7527 (mtmt)
REVERT: A 1002 MET cc_start: 0.6617 (mmm) cc_final: 0.6316 (mmm)
  outliers start: 37
  outliers final: 24
  residues processed: 186
  average time/residue: 0.0926
  time to fit residues: 21.9367
Evaluate side-chains
  180 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 TRP
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0980
   chunk 67 optimal weight:    0.4980
   chunk 29 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 6 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.163774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.137348 restraints weight = 11411.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.142062 restraints weight = 6494.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.145505 restraints weight = 4282.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.147793 restraints weight = 3097.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.149577 restraints weight = 2437.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6367  Z= 0.121
  Angle     :  0.635   6.909   8643  Z= 0.321
  Chirality :  0.042   0.147    966
  Planarity :  0.004   0.054   1042
  Dihedral  :  9.385  94.069    898
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 28.21 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.37 (0.33), residues: 722
  helix:  0.27 (0.28), residues: 352
  sheet: -1.39 (0.77), residues: 43
  loop : -0.53 (0.38), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 747 
 TYR   0.012   0.001   TYR A 707 
 PHE   0.020   0.001   PHE A 836 
 TRP   0.018   0.001   TRP A 288 
 HIS   0.005   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6367)
  covalent geometry    : angle       0.63505 ( 8643)
  hydrogen bonds       : bond        0.03805 (  244)
  hydrogen bonds       : angle       5.07714 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  479 GLU cc_start: 0.6989 (tp30) cc_final: 0.6653 (tp30)
REVERT: A  491 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8123 (m-80)
REVERT: A  536 MET cc_start: 0.7262 (ptp) cc_final: 0.6985 (ptp)
REVERT: A  539 ASP cc_start: 0.7990 (p0) cc_final: 0.7717 (p0)
REVERT: A  542 ILE cc_start: 0.8519 (mt) cc_final: 0.8297 (mt)
REVERT: A  560 HIS cc_start: 0.7669 (t-90) cc_final: 0.7143 (t-90)
REVERT: A  597 ILE cc_start: 0.7691 (mp) cc_final: 0.7354 (mm)
REVERT: A  607 LYS cc_start: 0.7663 (ttpt) cc_final: 0.7109 (tppt)
REVERT: A  608 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7731 (pp)
REVERT: A  654 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7676 (mptt)
REVERT: A  668 PHE cc_start: 0.8808 (t80) cc_final: 0.8574 (t80)
REVERT: A  672 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7808 (mm)
REVERT: A  673 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6482 (tm-30)
REVERT: A  705 ILE cc_start: 0.7324 (mt) cc_final: 0.6883 (pt)
REVERT: A  742 LEU cc_start: 0.8399 (tp) cc_final: 0.8119 (mp)
REVERT: A  746 ASN cc_start: 0.8093 (t0) cc_final: 0.7586 (p0)
REVERT: A  790 LYS cc_start: 0.8591 (ptpp) cc_final: 0.8147 (ptpp)
REVERT: A  793 LYS cc_start: 0.8943 (mttt) cc_final: 0.8415 (mttt)
REVERT: A  804 CYS cc_start: 0.2347 (OUTLIER) cc_final: 0.0764 (p)
REVERT: A  815 MET cc_start: 0.5384 (tmm) cc_final: 0.4552 (tmm)
REVERT: A  820 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7658 (tptt)
REVERT: A  823 TYR cc_start: 0.7880 (t80) cc_final: 0.7530 (t80)
REVERT: A  834 MET cc_start: 0.6757 (tmm) cc_final: 0.6206 (tmm)
REVERT: A  837 PHE cc_start: 0.7751 (m-80) cc_final: 0.6781 (m-80)
REVERT: A  876 LYS cc_start: 0.7788 (tptt) cc_final: 0.7556 (tptt)
REVERT: A  932 LEU cc_start: 0.2098 (OUTLIER) cc_final: 0.0526 (mt)
REVERT: A  939 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6217 (t0)
REVERT: A  949 LEU cc_start: 0.7454 (tt) cc_final: 0.6575 (mt)
REVERT: A 1002 MET cc_start: 0.6569 (mmm) cc_final: 0.6263 (mmm)
  outliers start: 36
  outliers final: 26
  residues processed: 175
  average time/residue: 0.1013
  time to fit residues: 22.5922
Evaluate side-chains
  188 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 155
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  766 ILE
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0870
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.162384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.135788 restraints weight = 11485.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.140520 restraints weight = 6443.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.144032 restraints weight = 4198.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.146335 restraints weight = 3011.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.148175 restraints weight = 2360.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6503
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6367  Z= 0.138
  Angle     :  0.640   9.106   8643  Z= 0.324
  Chirality :  0.043   0.286    966
  Planarity :  0.004   0.053   1042
  Dihedral  :  9.242  87.198    898
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 28.05 %
    Favored  : 65.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.37 (0.33), residues: 722
  helix:  0.31 (0.28), residues: 359
  sheet: -1.52 (0.76), residues: 43
  loop : -0.56 (0.39), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 680 
 TYR   0.019   0.001   TYR A 414 
 PHE   0.013   0.001   PHE A 759 
 TRP   0.017   0.002   TRP A 288 
 HIS   0.004   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6367)
  covalent geometry    : angle       0.63962 ( 8643)
  hydrogen bonds       : bond        0.03772 (  244)
  hydrogen bonds       : angle       5.00498 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 163
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.8813 (mmtp) cc_final: 0.8589 (mmtp)
REVERT: A  406 GLU cc_start: 0.7565 (pm20) cc_final: 0.7200 (pm20)
REVERT: A  479 GLU cc_start: 0.7026 (tp30) cc_final: 0.6446 (tp30)
REVERT: A  491 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8131 (m-80)
REVERT: A  523 ASP cc_start: 0.7705 (p0) cc_final: 0.7418 (p0)
REVERT: A  536 MET cc_start: 0.7272 (ptp) cc_final: 0.6936 (ptp)
REVERT: A  539 ASP cc_start: 0.8047 (p0) cc_final: 0.7490 (p0)
REVERT: A  542 ILE cc_start: 0.8510 (mt) cc_final: 0.8224 (mt)
REVERT: A  547 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7715 (mt)
REVERT: A  560 HIS cc_start: 0.7722 (t-90) cc_final: 0.7184 (t-90)
REVERT: A  578 LYS cc_start: 0.7804 (tttm) cc_final: 0.7394 (tttp)
REVERT: A  607 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7100 (tppt)
REVERT: A  617 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5741 (tp)
REVERT: A  654 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7681 (mptt)
REVERT: A  668 PHE cc_start: 0.8812 (t80) cc_final: 0.8585 (t80)
REVERT: A  672 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7832 (mm)
REVERT: A  673 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6653 (tm-30)
REVERT: A  705 ILE cc_start: 0.7406 (mt) cc_final: 0.6989 (pt)
REVERT: A  742 LEU cc_start: 0.8401 (tp) cc_final: 0.8122 (mp)
REVERT: A  745 ASN cc_start: 0.8392 (p0) cc_final: 0.8061 (m110)
REVERT: A  746 ASN cc_start: 0.8208 (t0) cc_final: 0.7486 (p0)
REVERT: A  789 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7126 (pp)
REVERT: A  790 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8153 (ptpp)
REVERT: A  793 LYS cc_start: 0.8961 (mttt) cc_final: 0.8423 (mttt)
REVERT: A  804 CYS cc_start: 0.2313 (OUTLIER) cc_final: 0.0699 (p)
REVERT: A  815 MET cc_start: 0.5398 (tmm) cc_final: 0.4573 (tmm)
REVERT: A  820 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7710 (tptt)
REVERT: A  823 TYR cc_start: 0.7911 (t80) cc_final: 0.7595 (t80)
REVERT: A  834 MET cc_start: 0.6780 (tmm) cc_final: 0.6352 (tmm)
REVERT: A  876 LYS cc_start: 0.7840 (tptt) cc_final: 0.7609 (tptt)
REVERT: A  919 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8097 (ttpt)
REVERT: A  932 LEU cc_start: 0.2187 (OUTLIER) cc_final: 0.0585 (mt)
REVERT: A  939 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6253 (t0)
REVERT: A  997 LYS cc_start: 0.8361 (tmtt) cc_final: 0.7601 (mtmt)
REVERT: A 1002 MET cc_start: 0.6623 (mmm) cc_final: 0.6316 (mmm)
REVERT: A 1040 PHE cc_start: 0.7519 (m-80) cc_final: 0.7280 (m-80)
  outliers start: 42
  outliers final: 25
  residues processed: 184
  average time/residue: 0.0926
  time to fit residues: 21.8016
Evaluate side-chains
  190 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  766 ILE
Chi-restraints excluded: chain A residue  783 GLU
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.159813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.133534 restraints weight = 11566.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.138169 restraints weight = 6594.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.141562 restraints weight = 4327.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.143649 restraints weight = 3119.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.145512 restraints weight = 2469.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6516
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6367  Z= 0.144
  Angle     :  0.683   9.607   8643  Z= 0.347
  Chirality :  0.044   0.290    966
  Planarity :  0.004   0.053   1042
  Dihedral  :  9.180  84.436    898
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 30.92 %
    Favored  : 64.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.35 (0.33), residues: 722
  helix:  0.28 (0.28), residues: 359
  sheet: -1.57 (0.76), residues: 43
  loop : -0.49 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 680 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.022   0.001   PHE A 836 
 TRP   0.016   0.001   TRP A 888 
 HIS   0.003   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6367)
  covalent geometry    : angle       0.68346 ( 8643)
  hydrogen bonds       : bond        0.03822 (  244)
  hydrogen bonds       : angle       5.02720 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7621 (pm20) cc_final: 0.7239 (pm20)
REVERT: A  479 GLU cc_start: 0.7074 (tp30) cc_final: 0.6452 (tp30)
REVERT: A  491 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8151 (m-80)
REVERT: A  523 ASP cc_start: 0.7742 (p0) cc_final: 0.7437 (p0)
REVERT: A  536 MET cc_start: 0.7257 (ptp) cc_final: 0.6926 (ptp)
REVERT: A  539 ASP cc_start: 0.8059 (p0) cc_final: 0.7526 (p0)
REVERT: A  542 ILE cc_start: 0.8519 (mt) cc_final: 0.8271 (mt)
REVERT: A  560 HIS cc_start: 0.7764 (t-90) cc_final: 0.6925 (t-90)
REVERT: A  578 LYS cc_start: 0.7802 (tttm) cc_final: 0.7557 (ttmm)
REVERT: A  607 LYS cc_start: 0.7606 (ttpt) cc_final: 0.7074 (tppt)
REVERT: A  617 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5933 (tp)
REVERT: A  654 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7685 (mptt)
REVERT: A  672 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7870 (mm)
REVERT: A  673 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6686 (tm-30)
REVERT: A  705 ILE cc_start: 0.7477 (mt) cc_final: 0.7084 (pt)
REVERT: A  742 LEU cc_start: 0.8406 (tp) cc_final: 0.8134 (mp)
REVERT: A  745 ASN cc_start: 0.8373 (p0) cc_final: 0.8079 (m110)
REVERT: A  746 ASN cc_start: 0.8214 (t0) cc_final: 0.7490 (p0)
REVERT: A  789 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7118 (pp)
REVERT: A  790 LYS cc_start: 0.8625 (ptpp) cc_final: 0.8200 (ptpp)
REVERT: A  793 LYS cc_start: 0.8965 (mttt) cc_final: 0.8437 (mttt)
REVERT: A  804 CYS cc_start: 0.2312 (OUTLIER) cc_final: 0.0690 (p)
REVERT: A  815 MET cc_start: 0.5455 (tmm) cc_final: 0.4624 (tmm)
REVERT: A  820 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7726 (tptt)
REVERT: A  823 TYR cc_start: 0.7892 (t80) cc_final: 0.7484 (t80)
REVERT: A  834 MET cc_start: 0.6886 (tmm) cc_final: 0.6250 (tmm)
REVERT: A  837 PHE cc_start: 0.7851 (m-80) cc_final: 0.6821 (m-80)
REVERT: A  876 LYS cc_start: 0.7846 (tptt) cc_final: 0.7615 (tptt)
REVERT: A  919 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8075 (ttpt)
REVERT: A  932 LEU cc_start: 0.2079 (OUTLIER) cc_final: 0.0495 (mt)
REVERT: A  939 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6276 (t0)
REVERT: A 1002 MET cc_start: 0.6629 (mmm) cc_final: 0.6327 (mmm)
REVERT: A 1040 PHE cc_start: 0.7579 (m-80) cc_final: 0.7338 (m-80)
  outliers start: 33
  outliers final: 22
  residues processed: 174
  average time/residue: 0.0983
  time to fit residues: 21.8000
Evaluate side-chains
  185 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  766 ILE
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:  100.0000
   chunk 67 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 610 GLN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.160967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.134779 restraints weight = 11517.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.139448 restraints weight = 6535.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.142787 restraints weight = 4269.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.144558 restraints weight = 3075.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.146556 restraints weight = 2472.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6502
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6367  Z= 0.141
  Angle     :  0.701   9.653   8643  Z= 0.353
  Chirality :  0.043   0.275    966
  Planarity :  0.005   0.054   1042
  Dihedral  :  9.111  83.749    898
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 31.37 %
    Favored  : 63.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.20 (0.33), residues: 722
  helix:  0.41 (0.28), residues: 347
  sheet: -1.61 (0.76), residues: 43
  loop : -0.37 (0.39), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 680 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.020   0.001   PHE A 836 
 TRP   0.016   0.002   TRP A 888 
 HIS   0.003   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6367)
  covalent geometry    : angle       0.70112 ( 8643)
  hydrogen bonds       : bond        0.03884 (  244)
  hydrogen bonds       : angle       5.07243 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7639 (pm20) cc_final: 0.7246 (pm20)
REVERT: A  479 GLU cc_start: 0.7075 (tp30) cc_final: 0.6483 (tp30)
REVERT: A  523 ASP cc_start: 0.7758 (p0) cc_final: 0.7473 (p0)
REVERT: A  536 MET cc_start: 0.7239 (ptp) cc_final: 0.6918 (ptp)
REVERT: A  539 ASP cc_start: 0.7952 (p0) cc_final: 0.7539 (p0)
REVERT: A  542 ILE cc_start: 0.8503 (mt) cc_final: 0.8290 (mt)
REVERT: A  560 HIS cc_start: 0.7730 (t-90) cc_final: 0.7041 (t-90)
REVERT: A  578 LYS cc_start: 0.7800 (tttm) cc_final: 0.7418 (tttp)
REVERT: A  607 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7362 (tppt)
REVERT: A  617 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.6002 (tp)
REVERT: A  651 PHE cc_start: 0.7352 (p90) cc_final: 0.6835 (p90)
REVERT: A  654 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7706 (mptt)
REVERT: A  672 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7876 (mm)
REVERT: A  673 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6657 (tm-30)
REVERT: A  705 ILE cc_start: 0.7472 (mt) cc_final: 0.7093 (pt)
REVERT: A  742 LEU cc_start: 0.8393 (tp) cc_final: 0.8126 (mp)
REVERT: A  745 ASN cc_start: 0.8345 (p0) cc_final: 0.8108 (m110)
REVERT: A  746 ASN cc_start: 0.8224 (t0) cc_final: 0.7482 (p0)
REVERT: A  790 LYS cc_start: 0.8579 (ptpp) cc_final: 0.8232 (ptpp)
REVERT: A  793 LYS cc_start: 0.8954 (mttt) cc_final: 0.8445 (mttt)
REVERT: A  804 CYS cc_start: 0.2329 (OUTLIER) cc_final: 0.0700 (p)
REVERT: A  815 MET cc_start: 0.5434 (tmm) cc_final: 0.4604 (tmm)
REVERT: A  820 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7695 (tptt)
REVERT: A  823 TYR cc_start: 0.7845 (t80) cc_final: 0.7459 (t80)
REVERT: A  834 MET cc_start: 0.6767 (tmm) cc_final: 0.6107 (tmm)
REVERT: A  837 PHE cc_start: 0.7680 (m-80) cc_final: 0.6773 (m-80)
REVERT: A  876 LYS cc_start: 0.7829 (tptt) cc_final: 0.7577 (tptt)
REVERT: A  880 LYS cc_start: 0.7436 (ttmm) cc_final: 0.6613 (mtmm)
REVERT: A  888 TRP cc_start: 0.7967 (t60) cc_final: 0.6646 (t60)
REVERT: A  919 LYS cc_start: 0.8535 (tmtt) cc_final: 0.8089 (ttpt)
REVERT: A  932 LEU cc_start: 0.2080 (OUTLIER) cc_final: 0.0479 (mt)
REVERT: A  939 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.5599 (t0)
REVERT: A  946 LYS cc_start: 0.8265 (tttt) cc_final: 0.8023 (tttp)
REVERT: A 1002 MET cc_start: 0.6608 (mmm) cc_final: 0.6323 (mmm)
REVERT: A 1040 PHE cc_start: 0.7583 (m-80) cc_final: 0.7337 (m-80)
REVERT: A 1058 LYS cc_start: 0.8154 (tppt) cc_final: 0.7735 (ttmm)
  outliers start: 32
  outliers final: 23
  residues processed: 179
  average time/residue: 0.0916
  time to fit residues: 20.9948
Evaluate side-chains
  188 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 TRP
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  766 ILE
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:  120.0000
   chunk 60 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 594 HIS
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.161494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.134806 restraints weight = 11552.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.139522 restraints weight = 6560.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.142935 restraints weight = 4293.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.145311 restraints weight = 3103.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.146907 restraints weight = 2424.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6367  Z= 0.159
  Angle     :  0.734   9.692   8643  Z= 0.372
  Chirality :  0.045   0.273    966
  Planarity :  0.005   0.052   1042
  Dihedral  :  9.099  83.687    898
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 31.52 %
    Favored  : 63.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.35 (0.33), residues: 722
  helix:  0.29 (0.28), residues: 355
  sheet: -1.70 (0.75), residues: 43
  loop : -0.48 (0.40), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 680 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.020   0.001   PHE A 836 
 TRP   0.017   0.002   TRP A 888 
 HIS   0.004   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6367)
  covalent geometry    : angle       0.73401 ( 8643)
  hydrogen bonds       : bond        0.03961 (  244)
  hydrogen bonds       : angle       5.18270 (  705)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7626 (pm20) cc_final: 0.7203 (pm20)
REVERT: A  479 GLU cc_start: 0.7100 (tp30) cc_final: 0.6549 (tp30)
REVERT: A  484 TYR cc_start: 0.6778 (m-10) cc_final: 0.6547 (m-10)
REVERT: A  491 PHE cc_start: 0.8499 (m-80) cc_final: 0.8291 (m-80)
REVERT: A  523 ASP cc_start: 0.7776 (p0) cc_final: 0.7485 (p0)
REVERT: A  536 MET cc_start: 0.7264 (ptp) cc_final: 0.6948 (ptp)
REVERT: A  539 ASP cc_start: 0.8034 (p0) cc_final: 0.7592 (p0)
REVERT: A  542 ILE cc_start: 0.8517 (mt) cc_final: 0.8293 (mt)
REVERT: A  545 LYS cc_start: 0.8585 (tttt) cc_final: 0.8308 (mttt)
REVERT: A  560 HIS cc_start: 0.7755 (t-90) cc_final: 0.7149 (t-90)
REVERT: A  578 LYS cc_start: 0.7820 (tttm) cc_final: 0.7382 (tttp)
REVERT: A  607 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7271 (tppt)
REVERT: A  617 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.6043 (tp)
REVERT: A  651 PHE cc_start: 0.7303 (p90) cc_final: 0.6805 (p90)
REVERT: A  654 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7705 (mptt)
REVERT: A  672 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7964 (mm)
REVERT: A  673 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6664 (tm-30)
REVERT: A  705 ILE cc_start: 0.7451 (mt) cc_final: 0.7080 (pt)
REVERT: A  742 LEU cc_start: 0.8425 (tp) cc_final: 0.8157 (mp)
REVERT: A  745 ASN cc_start: 0.8337 (p0) cc_final: 0.8103 (m110)
REVERT: A  746 ASN cc_start: 0.8234 (t0) cc_final: 0.7491 (p0)
REVERT: A  790 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8236 (ptpp)
REVERT: A  793 LYS cc_start: 0.8971 (mttt) cc_final: 0.8455 (mttt)
REVERT: A  804 CYS cc_start: 0.2362 (OUTLIER) cc_final: 0.0752 (p)
REVERT: A  815 MET cc_start: 0.5438 (tmm) cc_final: 0.4614 (tmm)
REVERT: A  820 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7767 (tptt)
REVERT: A  834 MET cc_start: 0.6770 (tmm) cc_final: 0.6140 (tmm)
REVERT: A  837 PHE cc_start: 0.7698 (m-80) cc_final: 0.6785 (m-80)
REVERT: A  876 LYS cc_start: 0.7880 (tptt) cc_final: 0.7671 (tptt)
REVERT: A  888 TRP cc_start: 0.8004 (t60) cc_final: 0.6652 (t60)
REVERT: A  919 LYS cc_start: 0.8559 (tmtt) cc_final: 0.8112 (ttpt)
REVERT: A  932 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.0479 (mt)
REVERT: A  939 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6666 (t0)
REVERT: A  965 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7735 (mmpt)
REVERT: A 1002 MET cc_start: 0.6652 (mmm) cc_final: 0.6370 (mmm)
REVERT: A 1040 PHE cc_start: 0.7623 (m-80) cc_final: 0.7389 (m-80)
REVERT: A 1058 LYS cc_start: 0.8178 (tppt) cc_final: 0.7741 (ttmm)
  outliers start: 32
  outliers final: 24
  residues processed: 185
  average time/residue: 0.0974
  time to fit residues: 23.0107
Evaluate side-chains
  196 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 TRP
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  766 ILE
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 52 optimal weight:   50.0000
   chunk 32 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 66 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
A 594 HIS
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.158128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.131672 restraints weight = 11466.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.136279 restraints weight = 6577.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.139737 restraints weight = 4354.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.142052 restraints weight = 3151.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.143134 restraints weight = 2475.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6367  Z= 0.168
  Angle     :  0.759   9.732   8643  Z= 0.383
  Chirality :  0.045   0.269    966
  Planarity :  0.005   0.049   1042
  Dihedral  :  9.084  83.845    898
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 31.98 %
    Favored  : 63.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.47 (0.33), residues: 722
  helix:  0.18 (0.28), residues: 357
  sheet: -1.65 (0.76), residues: 43
  loop : -0.53 (0.39), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1028 
 TYR   0.012   0.001   TYR A 785 
 PHE   0.019   0.002   PHE A 836 
 TRP   0.017   0.002   TRP A 888 
 HIS   0.009   0.002   HIS A 594 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6367)
  covalent geometry    : angle       0.75864 ( 8643)
  hydrogen bonds       : bond        0.03916 (  244)
  hydrogen bonds       : angle       5.21453 (  705)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1702.70 seconds
wall clock time: 30 minutes 5.77 seconds (1805.77 seconds total)