Starting phenix.real_space_refine
on Tue Aug  4 19:10:53 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_40859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_40859.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_40859.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_40859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_40859.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_40859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxu_40859/08_2026/8sxu_40859.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 10}
          Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 5}
          Link IDs: {'rna2p': 4, 'rna3p': 5}
  Time building chain proxies: 1.47, per 1000 atoms: 0.24
  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: 0.48
  Conformation dependent library (CDL) restraints added in 329.5 milliseconds
  

  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: 0.74
  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: 0.96

  Time building geometry restraints manager: 0.65 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: 8493
        2.13 -     4.27: 122
        4.27 -     6.40: 23
        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 -    17.67: 3191
       17.67 -    35.34: 497
       35.34 -    53.00: 120
       53.00 -    70.67: 48
       70.67 -    88.34: 14
  Dihedral angle restraints: 3870
    sinusoidal: 1722
      harmonic: 2148
  Sorted by residual:
  dihedral pdb=" C4'   A C   9 "
           pdb=" C3'   A C   9 "
           pdb=" C2'   A C   9 "
           pdb=" C1'   A C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.62   72.96     1      3.10e+00 1.04e-01 7.06e+02
  dihedral pdb=" C4'   A C  11 "
           pdb=" C3'   A C  11 "
           pdb=" C2'   A C  11 "
           pdb=" C1'   A C  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -35.26   71.61     1      3.10e+00 1.04e-01 6.84e+02
  dihedral pdb=" C4'   A C   2 "
           pdb=" C3'   A C   2 "
           pdb=" C2'   A C   2 "
           pdb=" C1'   A C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -34.34   70.69     1      3.10e+00 1.04e-01 6.69e+02
  ... (remaining 3867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 832
       0.060 -    0.119: 110
       0.119 -    0.178: 4
       0.178 -    0.238: 8
       0.238 -    0.297: 12
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" C2'   A C  10 "
            pdb=" C3'   A C  10 "
            pdb=" O2'   A C  10 "
            pdb=" C1'   A C  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.49   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" C2'   A C   9 "
            pdb=" C3'   A C   9 "
            pdb=" O2'   A C   9 "
            pdb=" C1'   A C   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.50   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" C2'   A C   7 "
            pdb=" C3'   A C   7 "
            pdb=" O2'   A C   7 "
            pdb=" C1'   A C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.51   -0.28 2.00e-01 2.50e+01 1.96e+00
  ... (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:             0.670
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.900
  Find NCS groups from input model:        0.030
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
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= 0.113
  Angle     :  0.623  10.665   8643  Z= 0.311
  Chirality :  0.053   0.297    966
  Planarity :  0.004   0.053   1042
  Dihedral  : 19.068  88.340   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 are 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/Z
  covalent geometry    : bond        0.00281 /  0.11 ( 6367)
  covalent geometry    : angle       0.62347 /  0.31 ( 8643)
  hydrogen bonds       : bond        0.28648 / 18.68 (  244)
  hydrogen bonds       : angle       8.20326 /  5.89 (  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  : 0.225 
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: 0.2803 (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: 0.8443 (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: 0.7535 (m-80) cc_final: 0.7024 (m-80)
REVERT: A  764 LYS cc_start: 0.6869 (tmmt) cc_final: 0.6667 (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: 0.5935 (tmm) cc_final: 0.5234 (tmm)
REVERT: A  823 TYR cc_start: 0.8195 (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: 0.0937
  time to fit residues: 20.9541
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  : 0.228 
-------------------------------------------------------------------------------
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...
A 450 ASN
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 GLN
A 581 ASN
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 669 ASN ** 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.162488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.135711 restraints weight = 11585.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.140378 restraints weight = 6630.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.143719 restraints weight = 4398.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.145875 restraints weight = 3220.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.147753 restraints weight = 2577.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6442
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6367  Z= 0.165
  Angle     :  0.762  11.401   8643  Z= 0.370
  Chirality :  0.056   0.416    966
  Planarity :  0.005   0.054   1042
  Dihedral  : 11.391 150.921    898
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 26.40 %
    Favored  : 68.17 %
  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 are not related in a simple way.
  whole: -0.35 (0.33), residues: 722
  helix:  0.19 (0.27), residues: 357
  sheet: -1.01 (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 550 
 TYR   0.011   0.001   TYR A1054 
 PHE   0.014   0.001   PHE A 781 
 TRP   0.030   0.002   TRP A 288 
 HIS   0.002   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 6367)
  covalent geometry    : angle       0.76196 /  0.37 ( 8643)
  hydrogen bonds       : bond        0.05161 /  3.47 (  244)
  hydrogen bonds       : angle       5.80273 /  4.10 (  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  : 0.210 
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: 0.8124 (OUTLIER) cc_final: 0.7870 (p)
REVERT: A  536 MET cc_start: 0.7218 (ptp) cc_final: 0.6879 (ptp)
REVERT: A  538 ILE cc_start: 0.7977 (mm) cc_final: 0.7676 (mp)
REVERT: A  539 ASP cc_start: 0.7997 (p0) cc_final: 0.7466 (p0)
REVERT: A  542 ILE cc_start: 0.8511 (mt) cc_final: 0.8304 (mt)
REVERT: A  547 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7643 (mt)
REVERT: A  560 HIS cc_start: 0.7104 (t-90) cc_final: 0.6848 (t-90)
REVERT: A  578 LYS cc_start: 0.7793 (tttp) cc_final: 0.7345 (tttp)
REVERT: A  627 LEU cc_start: 0.7334 (mt) cc_final: 0.6995 (mt)
REVERT: A  651 PHE cc_start: 0.7401 (p90) cc_final: 0.6667 (p90)
REVERT: A  654 LYS cc_start: 0.7865 (mmtp) cc_final: 0.7605 (mptt)
REVERT: A  666 LEU cc_start: 0.8717 (mm) cc_final: 0.8463 (mm)
REVERT: A  673 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6438 (tm-30)
REVERT: A  710 ASN cc_start: 0.8047 (t0) cc_final: 0.7625 (p0)
REVERT: A  759 PHE cc_start: 0.7200 (m-80) cc_final: 0.6494 (m-80)
REVERT: A  766 ILE cc_start: 0.7594 (pt) cc_final: 0.7240 (pt)
REVERT: A  772 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6388 (mm-40)
REVERT: A  789 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7021 (pp)
REVERT: A  790 LYS cc_start: 0.8625 (ptpp) cc_final: 0.7853 (ptpp)
REVERT: A  793 LYS cc_start: 0.8948 (mttt) cc_final: 0.8402 (mttt)
REVERT: A  815 MET cc_start: 0.5370 (tmm) cc_final: 0.4580 (tmm)
REVERT: A  823 TYR cc_start: 0.7808 (t80) cc_final: 0.7530 (t80)
REVERT: A  834 MET cc_start: 0.6890 (tmm) cc_final: 0.6586 (tmm)
REVERT: A  837 PHE cc_start: 0.7775 (m-80) cc_final: 0.7520 (m-80)
REVERT: A  876 LYS cc_start: 0.7696 (tptt) cc_final: 0.7404 (tptt)
REVERT: A  919 LYS cc_start: 0.8477 (tmtt) cc_final: 0.8103 (ttpt)
REVERT: A  939 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6511 (m-40)
REVERT: A 1058 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8085 (ttmm)
  outliers start: 36
  outliers final: 21
  residues processed: 189
  average time/residue: 0.0691
  time to fit residues: 16.9257
Evaluate side-chains
  166 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
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  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  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 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:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0770
   chunk 13 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4370 r_free = 0.4370 target = 0.163154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.137262 restraints weight = 11517.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.141838 restraints weight = 6583.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.145236 restraints weight = 4331.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.147562 restraints weight = 3129.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.148763 restraints weight = 2448.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6367  Z= 0.143
  Angle     :  0.711   9.129   8643  Z= 0.350
  Chirality :  0.052   0.495    966
  Planarity :  0.004   0.051   1042
  Dihedral  : 11.105 153.725    898
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 26.70 %
    Favored  : 68.17 %
  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 are not related in a simple way.
  whole: -0.49 (0.32), residues: 722
  helix:  0.19 (0.28), residues: 352
  sheet: -1.17 (0.83), residues: 43
  loop : -0.66 (0.38), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 631 
 TYR   0.009   0.001   TYR A1054 
 PHE   0.017   0.001   PHE A 781 
 TRP   0.020   0.002   TRP A 288 
 HIS   0.008   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 6367)
  covalent geometry    : angle       0.71106 /  0.35 ( 8643)
  hydrogen bonds       : bond        0.04507 /  2.98 (  244)
  hydrogen bonds       : angle       5.42946 /  3.83 (  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
  211 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 177
  time to evaluate  : 0.172 
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: 0.8142 (OUTLIER) cc_final: 0.7898 (p)
REVERT: A  491 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8217 (m-80)
REVERT: A  531 ARG cc_start: 0.3620 (mmt180) cc_final: 0.2867 (tpt170)
REVERT: A  536 MET cc_start: 0.7250 (ptp) cc_final: 0.6941 (ptp)
REVERT: A  538 ILE cc_start: 0.8037 (mm) cc_final: 0.7704 (mp)
REVERT: A  539 ASP cc_start: 0.8009 (p0) cc_final: 0.7667 (p0)
REVERT: A  542 ILE cc_start: 0.8502 (mt) cc_final: 0.8271 (mt)
REVERT: A  545 LYS cc_start: 0.8516 (tttt) cc_final: 0.8177 (mttt)
REVERT: A  560 HIS cc_start: 0.7115 (t-90) cc_final: 0.6875 (t-90)
REVERT: A  597 ILE cc_start: 0.7789 (mp) cc_final: 0.7313 (mm)
REVERT: A  627 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7030 (mt)
REVERT: A  651 PHE cc_start: 0.7415 (p90) cc_final: 0.6726 (p90)
REVERT: A  654 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7632 (mptt)
REVERT: A  666 LEU cc_start: 0.8688 (mm) cc_final: 0.8467 (mm)
REVERT: A  673 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6435 (tm-30)
REVERT: A  699 LEU cc_start: 0.7783 (mp) cc_final: 0.7547 (mp)
REVERT: A  710 ASN cc_start: 0.8006 (t0) cc_final: 0.7583 (p0)
REVERT: A  766 ILE cc_start: 0.7589 (pt) cc_final: 0.7223 (pt)
REVERT: A  772 GLN cc_start: 0.6860 (mm-40) cc_final: 0.6378 (mm110)
REVERT: A  789 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.6994 (pp)
REVERT: A  790 LYS cc_start: 0.8526 (ptpp) cc_final: 0.7810 (ptpp)
REVERT: A  793 LYS cc_start: 0.8923 (mttt) cc_final: 0.8390 (mttt)
REVERT: A  815 MET cc_start: 0.5300 (tmm) cc_final: 0.4499 (tmm)
REVERT: A  823 TYR cc_start: 0.7771 (t80) cc_final: 0.7460 (t80)
REVERT: A  834 MET cc_start: 0.6826 (tmm) cc_final: 0.6429 (tmm)
REVERT: A  876 LYS cc_start: 0.7736 (tptt) cc_final: 0.7532 (tptt)
REVERT: A  880 LYS cc_start: 0.7515 (ttmm) cc_final: 0.7121 (mmtt)
REVERT: A  939 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.6164 (t0)
  outliers start: 34
  outliers final: 18
  residues processed: 197
  average time/residue: 0.0663
  time to fit residues: 16.8039
Evaluate side-chains
  191 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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  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  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 1031 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 66 optimal weight:    0.0770
   chunk 14 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0970
   chunk 52 optimal weight:   40.0000
   chunk 6 optimal weight:   10.0000
   overall best weight:    0.4536

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 734 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 = 0.4361 r_free = 0.4361 target = 0.162660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.136289 restraints weight = 11494.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.141086 restraints weight = 6465.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.144293 restraints weight = 4192.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.146698 restraints weight = 3026.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.147964 restraints weight = 2357.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.2966

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= 0.130
  Angle     :  0.670   8.121   8643  Z= 0.330
  Chirality :  0.049   0.449    966
  Planarity :  0.004   0.054   1042
  Dihedral  : 10.788 155.839    898
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 28.36 %
    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 are not related in a simple way.
  whole: -0.34 (0.33), residues: 722
  helix:  0.32 (0.28), residues: 343
  sheet: -1.26 (0.80), residues: 43
  loop : -0.53 (0.38), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 631 
 TYR   0.023   0.001   TYR A 414 
 PHE   0.009   0.001   PHE A 836 
 TRP   0.027   0.002   TRP A 288 
 HIS   0.008   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 6367)
  covalent geometry    : angle       0.67040 /  0.33 ( 8643)
  hydrogen bonds       : bond        0.03877 /  2.52 (  244)
  hydrogen bonds       : angle       5.12434 /  3.62 (  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
  211 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 0.126 
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  405 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (p)
REVERT: A  428 GLU cc_start: 0.6735 (mp0) cc_final: 0.6483 (mp0)
REVERT: A  491 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8213 (m-80)
REVERT: A  531 ARG cc_start: 0.3428 (mmt180) cc_final: 0.2602 (tpt170)
REVERT: A  536 MET cc_start: 0.7266 (ptp) cc_final: 0.6961 (ptp)
REVERT: A  538 ILE cc_start: 0.7957 (mm) cc_final: 0.7644 (mp)
REVERT: A  539 ASP cc_start: 0.7986 (p0) cc_final: 0.7776 (p0)
REVERT: A  542 ILE cc_start: 0.8476 (mt) cc_final: 0.8248 (mt)
REVERT: A  545 LYS cc_start: 0.8482 (tttt) cc_final: 0.8175 (mttt)
REVERT: A  560 HIS cc_start: 0.7136 (t-90) cc_final: 0.6889 (t-90)
REVERT: A  597 ILE cc_start: 0.7681 (mp) cc_final: 0.7255 (mm)
REVERT: A  607 LYS cc_start: 0.7539 (pttm) cc_final: 0.7270 (tppt)
REVERT: A  640 ASN cc_start: 0.7656 (p0) cc_final: 0.7127 (p0)
REVERT: A  651 PHE cc_start: 0.7379 (p90) cc_final: 0.6775 (p90)
REVERT: A  654 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7658 (mptt)
REVERT: A  666 LEU cc_start: 0.8680 (mm) cc_final: 0.8416 (mm)
REVERT: A  673 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6466 (tm-30)
REVERT: A  742 LEU cc_start: 0.8383 (tp) cc_final: 0.8104 (mp)
REVERT: A  766 ILE cc_start: 0.7596 (pt) cc_final: 0.7287 (pt)
REVERT: A  772 GLN cc_start: 0.6868 (mm-40) cc_final: 0.6611 (mm-40)
REVERT: A  789 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7044 (pp)
REVERT: A  790 LYS cc_start: 0.8558 (ptpp) cc_final: 0.7927 (ptpp)
REVERT: A  793 LYS cc_start: 0.8939 (mttt) cc_final: 0.8402 (mttt)
REVERT: A  815 MET cc_start: 0.5373 (tmm) cc_final: 0.4540 (tmm)
REVERT: A  823 TYR cc_start: 0.7821 (t80) cc_final: 0.7575 (t80)
REVERT: A  834 MET cc_start: 0.6803 (tmm) cc_final: 0.6271 (tmm)
REVERT: A  837 PHE cc_start: 0.7734 (m-80) cc_final: 0.6914 (m-80)
REVERT: A  876 LYS cc_start: 0.7760 (tptt) cc_final: 0.7526 (tptt)
REVERT: A  880 LYS cc_start: 0.7468 (ttmm) cc_final: 0.7156 (mmtt)
REVERT: A  939 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6514 (t0)
REVERT: A  965 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7761 (mmtt)
REVERT: A 1058 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7849 (ttmm)
REVERT: A 1059 GLN cc_start: 0.7585 (pt0) cc_final: 0.7353 (pp30)
  outliers start: 35
  outliers final: 22
  residues processed: 194
  average time/residue: 0.0660
  time to fit residues: 16.4547
Evaluate side-chains
  196 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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  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  619 LYS
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  756 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  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
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  965 LYS
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:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0000
   chunk 11 optimal weight:    0.0980
   chunk 18 optimal weight:    7.9990
   chunk 66 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 594 HIS
A 900 ASN
** 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 = 0.4364 r_free = 0.4364 target = 0.163210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.136149 restraints weight = 11730.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.140846 restraints weight = 6692.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.144146 restraints weight = 4403.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.146581 restraints weight = 3203.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.148339 restraints weight = 2507.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6440
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6367  Z= 0.127
  Angle     :  0.660   7.523   8643  Z= 0.325
  Chirality :  0.048   0.325    966
  Planarity :  0.004   0.054   1042
  Dihedral  : 10.522 155.694    898
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.51 %
    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 are not related in a simple way.
  whole: -0.23 (0.33), residues: 722
  helix:  0.39 (0.28), residues: 343
  sheet: -1.21 (0.78), residues: 43
  loop : -0.46 (0.38), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 747 
 TYR   0.013   0.001   TYR A 414 
 PHE   0.008   0.001   PHE A 917 
 TRP   0.019   0.002   TRP A 288 
 HIS   0.007   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 6367)
  covalent geometry    : angle       0.66039 /  0.33 ( 8643)
  hydrogen bonds       : bond        0.03650 /  2.39 (  244)
  hydrogen bonds       : angle       5.01814 /  3.55 (  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
  204 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.216 
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  285 GLN cc_start: 0.7458 (mp10) cc_final: 0.6779 (mp10)
REVERT: A  405 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8024 (p)
REVERT: A  428 GLU cc_start: 0.6745 (mp0) cc_final: 0.6541 (mp0)
REVERT: A  479 GLU cc_start: 0.7031 (tp30) cc_final: 0.6820 (tp30)
REVERT: A  491 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8125 (m-80)
REVERT: A  531 ARG cc_start: 0.3017 (mmt180) cc_final: 0.2301 (tpt170)
REVERT: A  536 MET cc_start: 0.7254 (ptp) cc_final: 0.6923 (ptp)
REVERT: A  538 ILE cc_start: 0.7955 (mm) cc_final: 0.7653 (mp)
REVERT: A  539 ASP cc_start: 0.8079 (p0) cc_final: 0.7579 (p0)
REVERT: A  542 ILE cc_start: 0.8498 (mt) cc_final: 0.8279 (mt)
REVERT: A  560 HIS cc_start: 0.7223 (t-90) cc_final: 0.6922 (t-90)
REVERT: A  578 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7365 (tttp)
REVERT: A  597 ILE cc_start: 0.7696 (mp) cc_final: 0.7257 (mm)
REVERT: A  651 PHE cc_start: 0.7395 (p90) cc_final: 0.6812 (p90)
REVERT: A  654 LYS cc_start: 0.7932 (mmtp) cc_final: 0.7690 (mptt)
REVERT: A  668 PHE cc_start: 0.8806 (t80) cc_final: 0.8579 (t80)
REVERT: A  672 LEU cc_start: 0.8294 (mm) cc_final: 0.7830 (mm)
REVERT: A  673 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6553 (tm-30)
REVERT: A  742 LEU cc_start: 0.8413 (tp) cc_final: 0.8140 (mp)
REVERT: A  746 ASN cc_start: 0.8086 (t0) cc_final: 0.7456 (p0)
REVERT: A  766 ILE cc_start: 0.7551 (pt) cc_final: 0.7162 (pt)
REVERT: A  772 GLN cc_start: 0.6916 (mm-40) cc_final: 0.6481 (mm110)
REVERT: A  789 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7133 (pp)
REVERT: A  790 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8109 (ptpp)
REVERT: A  793 LYS cc_start: 0.8938 (mttt) cc_final: 0.8400 (mttt)
REVERT: A  804 CYS cc_start: 0.2340 (OUTLIER) cc_final: 0.0790 (p)
REVERT: A  815 MET cc_start: 0.5402 (tmm) cc_final: 0.4562 (tmm)
REVERT: A  823 TYR cc_start: 0.7854 (t80) cc_final: 0.7593 (t80)
REVERT: A  834 MET cc_start: 0.6826 (tmm) cc_final: 0.6286 (tmm)
REVERT: A  837 PHE cc_start: 0.7752 (m-80) cc_final: 0.6886 (m-80)
REVERT: A  876 LYS cc_start: 0.7771 (tptt) cc_final: 0.7531 (tptt)
REVERT: A  898 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7099 (tp40)
REVERT: A  932 LEU cc_start: 0.2082 (OUTLIER) cc_final: 0.0464 (mt)
REVERT: A  939 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6249 (t0)
REVERT: A  946 LYS cc_start: 0.8217 (tttt) cc_final: 0.7996 (tttp)
  outliers start: 33
  outliers final: 20
  residues processed: 190
  average time/residue: 0.0738
  time to fit residues: 18.0603
Evaluate side-chains
  192 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
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  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 1035 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0980
   chunk 6 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 784 ASN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.164637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.137781 restraints weight = 11437.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.142414 restraints weight = 6528.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.145763 restraints weight = 4307.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.148042 restraints weight = 3129.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.149766 restraints weight = 2467.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6454
moved from start:          0.3615

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= 0.131
  Angle     :  0.662   8.597   8643  Z= 0.325
  Chirality :  0.046   0.270    966
  Planarity :  0.004   0.054   1042
  Dihedral  : 10.414 156.067    898
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 29.56 %
    Favored  : 65.46 %
  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 are not related in a simple way.
  whole: -0.24 (0.33), residues: 722
  helix:  0.43 (0.28), residues: 350
  sheet: -1.39 (0.78), residues: 43
  loop : -0.51 (0.39), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 680 
 TYR   0.011   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.022   0.002   TRP A 288 
 HIS   0.005   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 6367)
  covalent geometry    : angle       0.66231 /  0.33 ( 8643)
  hydrogen bonds       : bond        0.03525 /  2.30 (  244)
  hydrogen bonds       : angle       4.97046 /  3.49 (  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
  209 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.128 
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  285 GLN cc_start: 0.7617 (mp10) cc_final: 0.7074 (mp10)
REVERT: A  428 GLU cc_start: 0.6784 (mp0) cc_final: 0.6508 (mp0)
REVERT: A  479 GLU cc_start: 0.7065 (tp30) cc_final: 0.6536 (tp30)
REVERT: A  491 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8111 (m-80)
REVERT: A  531 ARG cc_start: 0.2971 (mmt180) cc_final: 0.2229 (tpt170)
REVERT: A  536 MET cc_start: 0.7282 (ptp) cc_final: 0.6952 (ptp)
REVERT: A  538 ILE cc_start: 0.7961 (mm) cc_final: 0.7623 (mp)
REVERT: A  539 ASP cc_start: 0.8059 (p0) cc_final: 0.7781 (p0)
REVERT: A  542 ILE cc_start: 0.8479 (mt) cc_final: 0.8201 (mt)
REVERT: A  560 HIS cc_start: 0.7252 (t-90) cc_final: 0.6910 (t-90)
REVERT: A  578 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7473 (tttp)
REVERT: A  597 ILE cc_start: 0.7690 (mp) cc_final: 0.7377 (mm)
REVERT: A  607 LYS cc_start: 0.7720 (ttpt) cc_final: 0.6959 (tmmt)
REVERT: A  608 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7600 (pp)
REVERT: A  617 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5789 (tp)
REVERT: A  654 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7666 (mptt)
REVERT: A  668 PHE cc_start: 0.8783 (t80) cc_final: 0.8548 (t80)
REVERT: A  672 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7800 (mm)
REVERT: A  673 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6687 (tm-30)
REVERT: A  705 ILE cc_start: 0.7350 (mt) cc_final: 0.6892 (pt)
REVERT: A  742 LEU cc_start: 0.8399 (tp) cc_final: 0.8103 (mp)
REVERT: A  745 ASN cc_start: 0.8444 (p0) cc_final: 0.8131 (m110)
REVERT: A  746 ASN cc_start: 0.8106 (t0) cc_final: 0.7525 (p0)
REVERT: A  766 ILE cc_start: 0.7535 (pt) cc_final: 0.7157 (pt)
REVERT: A  772 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6439 (mm110)
REVERT: A  789 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7111 (pp)
REVERT: A  790 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8130 (ptpp)
REVERT: A  793 LYS cc_start: 0.8954 (mttt) cc_final: 0.8407 (mttt)
REVERT: A  804 CYS cc_start: 0.2330 (OUTLIER) cc_final: 0.0754 (p)
REVERT: A  815 MET cc_start: 0.5375 (tmm) cc_final: 0.4540 (tmm)
REVERT: A  820 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8055 (tptt)
REVERT: A  834 MET cc_start: 0.6829 (tmm) cc_final: 0.6247 (tmm)
REVERT: A  837 PHE cc_start: 0.7792 (m-80) cc_final: 0.6928 (m-80)
REVERT: A  876 LYS cc_start: 0.7789 (tptt) cc_final: 0.7551 (tptt)
REVERT: A  879 TYR cc_start: 0.8259 (t80) cc_final: 0.8029 (t80)
REVERT: A  898 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7014 (tm-30)
REVERT: A  919 LYS cc_start: 0.8543 (tmtt) cc_final: 0.8179 (tttt)
REVERT: A  939 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6292 (t0)
  outliers start: 33
  outliers final: 20
  residues processed: 192
  average time/residue: 0.0654
  time to fit residues: 16.2454
Evaluate side-chains
  201 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
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  491 PHE
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  608 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  675 LEU
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  708 LEU
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 1035 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0010
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0270
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0470
   overall best weight:    0.3542

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.163543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.137075 restraints weight = 11471.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.141752 restraints weight = 6503.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.145065 restraints weight = 4253.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.147473 restraints weight = 3083.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.149069 restraints weight = 2404.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.3831

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= 0.118
  Angle     :  0.650   8.638   8643  Z= 0.320
  Chirality :  0.046   0.268    966
  Planarity :  0.004   0.056   1042
  Dihedral  : 10.356 156.892    898
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 30.02 %
    Favored  : 65.31 %
  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 are not related in a simple way.
  whole: -0.20 (0.33), residues: 722
  helix:  0.45 (0.28), residues: 350
  sheet: -1.26 (0.81), residues: 43
  loop : -0.48 (0.39), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 765 
 TYR   0.017   0.001   TYR A 414 
 PHE   0.009   0.001   PHE A 291 
 TRP   0.017   0.001   TRP A 288 
 HIS   0.002   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 6367)
  covalent geometry    : angle       0.65008 /  0.32 ( 8643)
  hydrogen bonds       : bond        0.03504 /  2.27 (  244)
  hydrogen bonds       : angle       4.89246 /  3.42 (  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
  198 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  479 GLU cc_start: 0.7057 (tp30) cc_final: 0.6486 (tp30)
REVERT: A  491 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.8025 (m-80)
REVERT: A  531 ARG cc_start: 0.3033 (mmt180) cc_final: 0.2309 (tpt170)
REVERT: A  536 MET cc_start: 0.7229 (ptp) cc_final: 0.6926 (ptp)
REVERT: A  538 ILE cc_start: 0.7991 (mm) cc_final: 0.7665 (mp)
REVERT: A  539 ASP cc_start: 0.8114 (p0) cc_final: 0.7616 (p0)
REVERT: A  542 ILE cc_start: 0.8475 (mt) cc_final: 0.8246 (mt)
REVERT: A  547 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7627 (mt)
REVERT: A  560 HIS cc_start: 0.7203 (t-90) cc_final: 0.6968 (t-90)
REVERT: A  561 HIS cc_start: 0.8151 (p90) cc_final: 0.7804 (p90)
REVERT: A  578 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7441 (tttp)
REVERT: A  597 ILE cc_start: 0.7740 (mp) cc_final: 0.7526 (mp)
REVERT: A  607 LYS cc_start: 0.7620 (ttpt) cc_final: 0.6829 (tmmt)
REVERT: A  608 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7698 (pp)
REVERT: A  654 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7684 (mptt)
REVERT: A  668 PHE cc_start: 0.8816 (t80) cc_final: 0.8594 (t80)
REVERT: A  672 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7752 (mm)
REVERT: A  673 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6597 (tm-30)
REVERT: A  705 ILE cc_start: 0.7412 (mt) cc_final: 0.6990 (pt)
REVERT: A  742 LEU cc_start: 0.8434 (tp) cc_final: 0.8185 (mp)
REVERT: A  745 ASN cc_start: 0.8453 (p0) cc_final: 0.8211 (m110)
REVERT: A  746 ASN cc_start: 0.8323 (t0) cc_final: 0.7652 (p0)
REVERT: A  772 GLN cc_start: 0.6872 (mm-40) cc_final: 0.6458 (mm110)
REVERT: A  790 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8168 (ptpp)
REVERT: A  793 LYS cc_start: 0.8949 (mttt) cc_final: 0.8454 (mttt)
REVERT: A  804 CYS cc_start: 0.2267 (OUTLIER) cc_final: 0.0634 (p)
REVERT: A  815 MET cc_start: 0.5333 (tmm) cc_final: 0.4512 (tmm)
REVERT: A  820 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7966 (tptt)
REVERT: A  823 TYR cc_start: 0.7696 (t80) cc_final: 0.7417 (t80)
REVERT: A  834 MET cc_start: 0.6772 (tmm) cc_final: 0.6129 (tmm)
REVERT: A  837 PHE cc_start: 0.7744 (m-80) cc_final: 0.6876 (m-80)
REVERT: A  876 LYS cc_start: 0.7751 (tptt) cc_final: 0.7506 (tptt)
REVERT: A  898 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6985 (tm-30)
REVERT: A  906 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.3925 (tp30)
REVERT: A  919 LYS cc_start: 0.8550 (tmtt) cc_final: 0.8187 (tttt)
REVERT: A  939 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6282 (t0)
REVERT: A  975 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7573 (mmtm)
REVERT: A  978 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7630 (mt-10)
  outliers start: 31
  outliers final: 20
  residues processed: 184
  average time/residue: 0.0664
  time to fit residues: 15.7983
Evaluate side-chains
  192 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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  491 PHE
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  675 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  708 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  906 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0970
   chunk 14 optimal weight:    0.0070
   chunk 12 optimal weight:    0.0010
   chunk 49 optimal weight:    0.6980
   chunk 58 optimal weight:    0.1980
   chunk 33 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.1802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.166012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.138393 restraints weight = 11500.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.143255 restraints weight = 6614.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.146788 restraints weight = 4385.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.148821 restraints weight = 3200.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.150704 restraints weight = 2569.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6413
moved from start:          0.4009

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= 0.115
  Angle     :  0.664   9.945   8643  Z= 0.325
  Chirality :  0.045   0.267    966
  Planarity :  0.004   0.058   1042
  Dihedral  : 10.436 158.620    898
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 30.62 %
    Favored  : 64.56 %
  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 are not related in a simple way.
  whole: -0.21 (0.33), residues: 722
  helix:  0.41 (0.28), residues: 356
  sheet: -1.17 (0.82), residues: 43
  loop : -0.49 (0.39), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 483 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.010   0.001   PHE A 291 
 TRP   0.016   0.001   TRP A 288 
 HIS   0.003   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.11 ( 6367)
  covalent geometry    : angle       0.66354 /  0.33 ( 8643)
  hydrogen bonds       : bond        0.03345 /  2.16 (  244)
  hydrogen bonds       : angle       4.85898 /  3.41 (  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
  199 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7770 (mp10) cc_final: 0.6861 (mp10)
REVERT: A  479 GLU cc_start: 0.6955 (tp30) cc_final: 0.6339 (tp30)
REVERT: A  511 GLU cc_start: 0.4692 (OUTLIER) cc_final: 0.4465 (pp20)
REVERT: A  536 MET cc_start: 0.7172 (ptp) cc_final: 0.6846 (ptp)
REVERT: A  538 ILE cc_start: 0.7911 (mm) cc_final: 0.7593 (mp)
REVERT: A  539 ASP cc_start: 0.8120 (p0) cc_final: 0.7661 (p0)
REVERT: A  542 ILE cc_start: 0.8452 (mt) cc_final: 0.8228 (mt)
REVERT: A  560 HIS cc_start: 0.7273 (t-90) cc_final: 0.6805 (t-90)
REVERT: A  561 HIS cc_start: 0.8147 (p90) cc_final: 0.7918 (p90)
REVERT: A  578 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7259 (tttp)
REVERT: A  597 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7403 (mp)
REVERT: A  607 LYS cc_start: 0.7460 (ttpt) cc_final: 0.7032 (tmmt)
REVERT: A  608 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7510 (pp)
REVERT: A  617 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5711 (tp)
REVERT: A  654 LYS cc_start: 0.7895 (mmtp) cc_final: 0.7664 (mptt)
REVERT: A  668 PHE cc_start: 0.8785 (t80) cc_final: 0.8579 (t80)
REVERT: A  672 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7722 (mm)
REVERT: A  673 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6758 (tm-30)
REVERT: A  705 ILE cc_start: 0.7401 (mt) cc_final: 0.6924 (pt)
REVERT: A  742 LEU cc_start: 0.8459 (tp) cc_final: 0.8213 (mp)
REVERT: A  745 ASN cc_start: 0.8466 (p0) cc_final: 0.8198 (m110)
REVERT: A  746 ASN cc_start: 0.8280 (t0) cc_final: 0.7631 (p0)
REVERT: A  756 GLU cc_start: 0.7629 (pp20) cc_final: 0.6970 (tt0)
REVERT: A  764 LYS cc_start: 0.7410 (tmtt) cc_final: 0.7090 (tptp)
REVERT: A  772 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6443 (mm110)
REVERT: A  790 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8225 (ptpp)
REVERT: A  793 LYS cc_start: 0.8974 (mttt) cc_final: 0.8463 (mttt)
REVERT: A  804 CYS cc_start: 0.2351 (OUTLIER) cc_final: 0.0783 (p)
REVERT: A  815 MET cc_start: 0.5419 (tmm) cc_final: 0.4595 (tmm)
REVERT: A  820 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8053 (tptt)
REVERT: A  823 TYR cc_start: 0.7843 (t80) cc_final: 0.7458 (t80)
REVERT: A  834 MET cc_start: 0.6868 (tmm) cc_final: 0.6237 (tmm)
REVERT: A  837 PHE cc_start: 0.7900 (m-80) cc_final: 0.7014 (m-80)
REVERT: A  876 LYS cc_start: 0.7796 (tptt) cc_final: 0.7591 (tptt)
REVERT: A  898 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6957 (tp40)
REVERT: A  919 LYS cc_start: 0.8469 (tmtt) cc_final: 0.8108 (tttt)
REVERT: A  932 LEU cc_start: 0.1950 (OUTLIER) cc_final: 0.0472 (mt)
  outliers start: 32
  outliers final: 17
  residues processed: 184
  average time/residue: 0.0760
  time to fit residues: 17.9073
Evaluate side-chains
  183 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  511 GLU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  608 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  675 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  708 LEU
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  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
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:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 0 optimal weight:  120.0000
   chunk 67 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0870
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.163707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.136915 restraints weight = 11593.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.141683 restraints weight = 6595.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.145078 restraints weight = 4318.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.147379 restraints weight = 3115.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.149126 restraints weight = 2449.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6367  Z= 0.129
  Angle     :  0.682   9.673   8643  Z= 0.338
  Chirality :  0.046   0.266    966
  Planarity :  0.004   0.056   1042
  Dihedral  : 10.315 160.414    898
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 31.37 %
    Favored  : 64.71 %
  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 are not related in a simple way.
  whole: -0.38 (0.33), residues: 722
  helix:  0.21 (0.28), residues: 362
  sheet: -1.21 (0.81), residues: 43
  loop : -0.51 (0.40), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 765 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.015   0.001   PHE A 836 
 TRP   0.017   0.001   TRP A 288 
 HIS   0.002   0.001   HIS A 585 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 6367)
  covalent geometry    : angle       0.68246 /  0.34 ( 8643)
  hydrogen bonds       : bond        0.03292 /  2.18 (  244)
  hydrogen bonds       : angle       4.89404 /  3.44 (  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
  188 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7893 (mp10) cc_final: 0.7370 (mp10)
REVERT: A  479 GLU cc_start: 0.6931 (tp30) cc_final: 0.6341 (tp30)
REVERT: A  536 MET cc_start: 0.7239 (ptp) cc_final: 0.6799 (ptp)
REVERT: A  538 ILE cc_start: 0.7935 (mm) cc_final: 0.7634 (mp)
REVERT: A  539 ASP cc_start: 0.8177 (p0) cc_final: 0.7641 (p0)
REVERT: A  542 ILE cc_start: 0.8450 (mt) cc_final: 0.8245 (mt)
REVERT: A  562 ASP cc_start: 0.7750 (m-30) cc_final: 0.7547 (p0)
REVERT: A  578 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7386 (tttp)
REVERT: A  597 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7474 (mp)
REVERT: A  607 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6866 (ttpt)
REVERT: A  608 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7587 (pp)
REVERT: A  617 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5813 (tp)
REVERT: A  651 PHE cc_start: 0.7398 (p90) cc_final: 0.6872 (p90)
REVERT: A  654 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7678 (mptt)
REVERT: A  672 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7922 (mm)
REVERT: A  673 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6687 (tm-30)
REVERT: A  705 ILE cc_start: 0.7435 (mt) cc_final: 0.6974 (pt)
REVERT: A  737 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8033 (tppt)
REVERT: A  742 LEU cc_start: 0.8492 (tp) cc_final: 0.8275 (mp)
REVERT: A  745 ASN cc_start: 0.8475 (p0) cc_final: 0.8182 (m110)
REVERT: A  746 ASN cc_start: 0.8342 (t0) cc_final: 0.7724 (p0)
REVERT: A  756 GLU cc_start: 0.7596 (pp20) cc_final: 0.6947 (tt0)
REVERT: A  764 LYS cc_start: 0.7421 (tmtt) cc_final: 0.5971 (tptp)
REVERT: A  772 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6490 (mm110)
REVERT: A  790 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8269 (ptpp)
REVERT: A  793 LYS cc_start: 0.8977 (mttt) cc_final: 0.8483 (mttt)
REVERT: A  804 CYS cc_start: 0.2318 (OUTLIER) cc_final: 0.0757 (p)
REVERT: A  815 MET cc_start: 0.5374 (tmm) cc_final: 0.4556 (tmm)
REVERT: A  820 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8051 (tptt)
REVERT: A  834 MET cc_start: 0.6798 (tmm) cc_final: 0.6150 (tmm)
REVERT: A  837 PHE cc_start: 0.7896 (m-80) cc_final: 0.6987 (m-80)
REVERT: A  876 LYS cc_start: 0.7816 (tptt) cc_final: 0.7592 (tptt)
REVERT: A  898 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6940 (tm-30)
REVERT: A  919 LYS cc_start: 0.8512 (tmtt) cc_final: 0.8164 (tttt)
  outliers start: 26
  outliers final: 16
  residues processed: 174
  average time/residue: 0.0750
  time to fit residues: 16.6185
Evaluate side-chains
  182 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 159
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
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  597 ILE
Chi-restraints excluded: chain A residue  608 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  708 LEU
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  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
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:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:  120.0000
   chunk 60 optimal weight:    0.1980
   chunk 72 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0170
   chunk 69 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 851 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.163768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.136687 restraints weight = 11571.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.141435 restraints weight = 6569.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.145005 restraints weight = 4303.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.147355 restraints weight = 3070.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.149188 restraints weight = 2403.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6422
moved from start:          0.4342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6367  Z= 0.129
  Angle     :  0.702   8.995   8643  Z= 0.352
  Chirality :  0.046   0.266    966
  Planarity :  0.005   0.055   1042
  Dihedral  : 10.272 161.008    898
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 31.22 %
    Favored  : 65.01 %
  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 are not related in a simple way.
  whole: -0.26 (0.33), residues: 722
  helix:  0.33 (0.29), residues: 349
  sheet: -1.25 (0.83), residues: 43
  loop : -0.44 (0.39), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 765 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.018   0.001   PHE A 291 
 TRP   0.038   0.002   TRP A 573 
 HIS   0.002   0.001   HIS A 560 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 6367)
  covalent geometry    : angle       0.70202 /  0.35 ( 8643)
  hydrogen bonds       : bond        0.03286 /  2.17 (  244)
  hydrogen bonds       : angle       4.97812 /  3.49 (  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
  189 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7932 (mp10) cc_final: 0.7254 (mp10)
REVERT: A  445 GLU cc_start: 0.8111 (mp0) cc_final: 0.6900 (mp0)
REVERT: A  479 GLU cc_start: 0.6923 (tp30) cc_final: 0.6366 (tp30)
REVERT: A  484 TYR cc_start: 0.6765 (m-10) cc_final: 0.6513 (m-10)
REVERT: A  536 MET cc_start: 0.7262 (ptp) cc_final: 0.6808 (ptp)
REVERT: A  538 ILE cc_start: 0.7924 (mm) cc_final: 0.7537 (mp)
REVERT: A  539 ASP cc_start: 0.8126 (p0) cc_final: 0.7874 (p0)
REVERT: A  542 ILE cc_start: 0.8437 (mt) cc_final: 0.8234 (mt)
REVERT: A  578 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7375 (tttp)
REVERT: A  597 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7524 (mp)
REVERT: A  607 LYS cc_start: 0.7487 (ttpt) cc_final: 0.7006 (tmmt)
REVERT: A  608 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7667 (pp)
REVERT: A  617 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5853 (tp)
REVERT: A  651 PHE cc_start: 0.7323 (p90) cc_final: 0.6805 (p90)
REVERT: A  654 LYS cc_start: 0.7892 (mmtp) cc_final: 0.7686 (mptt)
REVERT: A  672 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7893 (mm)
REVERT: A  673 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6654 (tm-30)
REVERT: A  705 ILE cc_start: 0.7446 (mt) cc_final: 0.7009 (pt)
REVERT: A  742 LEU cc_start: 0.8488 (tp) cc_final: 0.8277 (mp)
REVERT: A  746 ASN cc_start: 0.8358 (t0) cc_final: 0.7773 (p0)
REVERT: A  756 GLU cc_start: 0.7596 (pp20) cc_final: 0.7229 (tm-30)
REVERT: A  772 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6512 (mm110)
REVERT: A  790 LYS cc_start: 0.8567 (ptpp) cc_final: 0.8249 (ptpp)
REVERT: A  793 LYS cc_start: 0.8972 (mttt) cc_final: 0.8484 (mttt)
REVERT: A  804 CYS cc_start: 0.2349 (OUTLIER) cc_final: 0.0769 (p)
REVERT: A  815 MET cc_start: 0.5373 (tmm) cc_final: 0.4554 (tmm)
REVERT: A  820 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8051 (tptt)
REVERT: A  834 MET cc_start: 0.6756 (tmm) cc_final: 0.6115 (tmm)
REVERT: A  837 PHE cc_start: 0.7828 (m-80) cc_final: 0.6930 (m-80)
REVERT: A  876 LYS cc_start: 0.7818 (tptt) cc_final: 0.7605 (tptt)
REVERT: A  898 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6936 (tm-30)
REVERT: A  919 LYS cc_start: 0.8525 (tmtt) cc_final: 0.8182 (tttt)
  outliers start: 25
  outliers final: 16
  residues processed: 174
  average time/residue: 0.0693
  time to fit residues: 15.5332
Evaluate side-chains
  188 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  608 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  708 LEU
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 1035 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 32 optimal weight:    0.6980
   chunk 53 optimal weight:    0.2980
   chunk 39 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 933 ASN
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.163462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.135736 restraints weight = 11642.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.140487 restraints weight = 6729.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.144130 restraints weight = 4503.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.146351 restraints weight = 3302.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.147646 restraints weight = 2643.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6367  Z= 0.141
  Angle     :  0.715  10.098   8643  Z= 0.360
  Chirality :  0.047   0.262    966
  Planarity :  0.005   0.052   1042
  Dihedral  : 10.278 162.379    898
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 31.67 %
    Favored  : 65.01 %
  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 are not related in a simple way.
  whole: -0.39 (0.33), residues: 722
  helix:  0.25 (0.28), residues: 357
  sheet: -1.30 (0.82), residues: 43
  loop : -0.56 (0.39), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1028 
 TYR   0.014   0.001   TYR A1054 
 PHE   0.016   0.001   PHE A 291 
 TRP   0.049   0.002   TRP A 573 
 HIS   0.003   0.001   HIS A 561 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 6367)
  covalent geometry    : angle       0.71535 /  0.36 ( 8643)
  hydrogen bonds       : bond        0.03291 /  2.19 (  244)
  hydrogen bonds       : angle       5.02671 /  3.55 (  705)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1396.60 seconds
wall clock time: 24 minutes 36.34 seconds (1476.34 seconds total)