Starting phenix.real_space_refine
on Sat May 10 12:42:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxu_40859/05_2025/8sxu_40859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxu_40859/05_2025/8sxu_40859.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxu_40859/05_2025/8sxu_40859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxu_40859/05_2025/8sxu_40859.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxu_40859/05_2025/8sxu_40859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxu_40859/05_2025/8sxu_40859.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6207
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5987
          Classifications: {'peptide': 726}
          Link IDs: {'PTRANS': 33, 'TRANS': 692}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 220
          Classifications: {'RNA': 10}
          Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 5}
          Link IDs: {'rna2p': 4, 'rna3p': 5}
  Time building chain proxies: 5.86, per 1000 atoms: 0.94
  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: 1.39
  Conformation dependent library (CDL) restraints added in 940.4 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: 1.86
  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: 1.79

  Time building geometry restraints manager: 1.76 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  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:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.960
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6592
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.099   6367  Z= 0.108
  Angle     :  0.571  10.665   8643  Z= 0.291
  Chirality :  0.039   0.139    966
  Planarity :  0.004   0.053   1042
  Dihedral  : 18.376 125.781   2474
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 15.99
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (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
 TRP   0.037   0.002   TRP A 288 
 HIS   0.002   0.001   HIS A 910 
 PHE   0.020   0.001   PHE A 651 
 TYR   0.005   0.001   TYR A 912 
 ARG   0.003   0.000   ARG A 577 

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

*********************** 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  : 0.712 
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  266 MET cc_start: 0.3185 (mmt) cc_final: 0.2803 (mmt)
REVERT: A  288 TRP cc_start: 0.7789 (t-100) cc_final: 0.7409 (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: 0.6520 (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: 0.7536 (m-80) cc_final: 0.7025 (m-80)
REVERT: A  764 LYS cc_start: 0.6870 (tmmt) cc_final: 0.6668 (tmtt)
REVERT: A  766 ILE cc_start: 0.7469 (pt) cc_final: 0.6724 (pt)
REVERT: A  772 GLN cc_start: 0.6497 (mm-40) cc_final: 0.6252 (mm110)
REVERT: A  791 GLU cc_start: 0.8402 (tp30) cc_final: 0.8090 (tp30)
REVERT: A  815 MET cc_start: 0.5936 (tmm) cc_final: 0.5234 (tmm)
REVERT: A  823 TYR cc_start: 0.8196 (t80) cc_final: 0.7947 (t80)
REVERT: A  876 LYS cc_start: 0.7527 (tptt) cc_final: 0.7320 (tptt)
REVERT: A  883 VAL cc_start: 0.8772 (t) cc_final: 0.8538 (t)
REVERT: A  919 LYS cc_start: 0.7805 (tmtt) cc_final: 0.7560 (ttpt)
REVERT: A  986 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8036 (pp30)
REVERT: A  997 LYS cc_start: 0.7507 (ttmm) cc_final: 0.7254 (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: 0.2133
  time to fit residues: 47.0551
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  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0060
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0970
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN
A 618 ASN
** 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.166512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.138913 restraints weight = 11486.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.143632 restraints weight = 6684.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.146853 restraints weight = 4504.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6498
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6367  Z= 0.131
  Angle     :  0.634   7.607   8643  Z= 0.325
  Chirality :  0.042   0.163    966
  Planarity :  0.005   0.054   1042
  Dihedral  :  9.976 120.622    898
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 26.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.33), residues: 722
  helix:  0.23 (0.27), residues: 351
  sheet: -0.93 (0.85), residues: 43
  loop : -0.50 (0.39), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 288 
 HIS   0.002   0.001   HIS A 585 
 PHE   0.015   0.001   PHE A 781 
 TYR   0.011   0.001   TYR A1054 
 ARG   0.003   0.001   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04947 (  244)
  hydrogen bonds       : angle       5.77683 (  705)
  covalent geometry    : bond        0.00293 ( 6367)
  covalent geometry    : angle       0.63356 ( 8643)

*********************** 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
  197 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.665 
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: 0.8116 (OUTLIER) cc_final: 0.7868 (p)
REVERT: A  536 MET cc_start: 0.7191 (ptp) cc_final: 0.6899 (ptp)
REVERT: A  538 ILE cc_start: 0.7996 (mm) cc_final: 0.7685 (mp)
REVERT: A  539 ASP cc_start: 0.7970 (p0) cc_final: 0.7469 (p0)
REVERT: A  542 ILE cc_start: 0.8529 (mt) cc_final: 0.8301 (mt)
REVERT: A  545 LYS cc_start: 0.8499 (tttt) cc_final: 0.8183 (mttt)
REVERT: A  547 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7633 (mt)
REVERT: A  552 GLN cc_start: 0.7159 (tp-100) cc_final: 0.6948 (tt0)
REVERT: A  596 ILE cc_start: 0.7630 (mm) cc_final: 0.7386 (tt)
REVERT: A  607 LYS cc_start: 0.7524 (pttm) cc_final: 0.7064 (ttpt)
REVERT: A  627 LEU cc_start: 0.7290 (mt) cc_final: 0.6920 (mt)
REVERT: A  651 PHE cc_start: 0.7285 (p90) cc_final: 0.6570 (p90)
REVERT: A  654 LYS cc_start: 0.7938 (mmtp) cc_final: 0.7684 (mptt)
REVERT: A  663 LEU cc_start: 0.8322 (tp) cc_final: 0.8076 (pt)
REVERT: A  666 LEU cc_start: 0.8685 (mm) cc_final: 0.8436 (mm)
REVERT: A  673 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6397 (tm-30)
REVERT: A  710 ASN cc_start: 0.8048 (t0) cc_final: 0.7700 (p0)
REVERT: A  720 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8488 (mtmm)
REVERT: A  759 PHE cc_start: 0.7005 (m-80) cc_final: 0.6228 (m-80)
REVERT: A  766 ILE cc_start: 0.7745 (pt) cc_final: 0.7448 (pt)
REVERT: A  772 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6403 (mm-40)
REVERT: A  789 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.6896 (pp)
REVERT: A  790 LYS cc_start: 0.8525 (ptpp) cc_final: 0.7757 (ptpp)
REVERT: A  793 LYS cc_start: 0.8944 (mttt) cc_final: 0.8390 (mttt)
REVERT: A  815 MET cc_start: 0.5322 (tmm) cc_final: 0.4532 (tmm)
REVERT: A  823 TYR cc_start: 0.7537 (t80) cc_final: 0.7270 (t80)
REVERT: A  834 MET cc_start: 0.6931 (tmm) cc_final: 0.6614 (tmm)
REVERT: A  837 PHE cc_start: 0.7687 (m-80) cc_final: 0.7451 (m-80)
REVERT: A  876 LYS cc_start: 0.7638 (tptt) cc_final: 0.7358 (tptt)
REVERT: A  919 LYS cc_start: 0.8518 (tmtt) cc_final: 0.8189 (ttpt)
REVERT: A 1017 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6962 (ptpp)
REVERT: A 1058 LYS cc_start: 0.8322 (ttmm) cc_final: 0.8096 (ttmm)
  outliers start: 33
  outliers final: 20
  residues processed: 189
  average time/residue: 0.2068
  time to fit residues: 49.8139
Evaluate side-chains
  178 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
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  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  954 THR
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1031 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0670
   chunk 9 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 669 ASN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1055 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.161986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.135827 restraints weight = 11515.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.140675 restraints weight = 6520.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.144019 restraints weight = 4247.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.2322

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= 0.138
  Angle     :  0.626   7.811   8643  Z= 0.321
  Chirality :  0.042   0.161    966
  Planarity :  0.004   0.051   1042
  Dihedral  :  9.910 117.001    898
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 27.15 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.32), residues: 722
  helix:  0.21 (0.28), residues: 352
  sheet: -1.16 (0.82), residues: 43
  loop : -0.69 (0.37), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 288 
 HIS   0.002   0.001   HIS A 561 
 PHE   0.014   0.001   PHE A 781 
 TYR   0.009   0.001   TYR A1054 
 ARG   0.008   0.001   ARG A 747 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04480 (  244)
  hydrogen bonds       : angle       5.44897 (  705)
  covalent geometry    : bond        0.00295 ( 6367)
  covalent geometry    : angle       0.62574 ( 8643)

*********************** 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
  201 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 167
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 TRP cc_start: 0.7747 (t-100) cc_final: 0.7435 (t-100)
REVERT: A  292 LYS cc_start: 0.8438 (mttp) cc_final: 0.8129 (mttp)
REVERT: A  405 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7917 (p)
REVERT: A  428 GLU cc_start: 0.6874 (mp0) cc_final: 0.6567 (mp0)
REVERT: A  491 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8275 (m-80)
REVERT: A  531 ARG cc_start: 0.3514 (mmt180) cc_final: 0.2754 (tpt170)
REVERT: A  536 MET cc_start: 0.7232 (ptp) cc_final: 0.6878 (ptp)
REVERT: A  538 ILE cc_start: 0.8047 (mm) cc_final: 0.7702 (mp)
REVERT: A  542 ILE cc_start: 0.8492 (mt) cc_final: 0.8272 (mt)
REVERT: A  545 LYS cc_start: 0.8513 (tttt) cc_final: 0.8212 (mttt)
REVERT: A  560 HIS cc_start: 0.7416 (t-90) cc_final: 0.6649 (t-90)
REVERT: A  578 LYS cc_start: 0.7776 (tttm) cc_final: 0.7379 (tttp)
REVERT: A  597 ILE cc_start: 0.7750 (mp) cc_final: 0.7300 (mm)
REVERT: A  640 ASN cc_start: 0.7679 (p0) cc_final: 0.7403 (p0)
REVERT: A  651 PHE cc_start: 0.7443 (p90) cc_final: 0.6712 (p90)
REVERT: A  654 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7622 (mptt)
REVERT: A  666 LEU cc_start: 0.8712 (mm) cc_final: 0.8481 (mm)
REVERT: A  673 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6596 (tm-30)
REVERT: A  710 ASN cc_start: 0.8001 (t0) cc_final: 0.7614 (p0)
REVERT: A  720 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8525 (mtmm)
REVERT: A  766 ILE cc_start: 0.7661 (pt) cc_final: 0.7346 (pt)
REVERT: A  772 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6552 (mm-40)
REVERT: A  789 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7065 (pp)
REVERT: A  790 LYS cc_start: 0.8575 (ptpp) cc_final: 0.7883 (ptpp)
REVERT: A  793 LYS cc_start: 0.8967 (mttt) cc_final: 0.8410 (mttt)
REVERT: A  815 MET cc_start: 0.5480 (tmm) cc_final: 0.4671 (tmm)
REVERT: A  823 TYR cc_start: 0.7822 (t80) cc_final: 0.7537 (t80)
REVERT: A  834 MET cc_start: 0.6971 (tmm) cc_final: 0.6584 (tmm)
REVERT: A  876 LYS cc_start: 0.7768 (tptt) cc_final: 0.7538 (tptt)
REVERT: A  939 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6522 (m-40)
REVERT: A  949 LEU cc_start: 0.7398 (tt) cc_final: 0.6336 (mt)
REVERT: A 1002 MET cc_start: 0.6556 (mmm) cc_final: 0.6354 (mmm)
  outliers start: 34
  outliers final: 24
  residues processed: 188
  average time/residue: 0.2082
  time to fit residues: 49.5920
Evaluate side-chains
  193 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
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  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  675 LEU
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  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 19 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0670
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 933 ASN ** 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 = 0.4369 r_free = 0.4369 target = 0.162842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.136697 restraints weight = 11633.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.141464 restraints weight = 6536.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.144924 restraints weight = 4251.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.2708

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= 0.129
  Angle     :  0.609   7.705   8643  Z= 0.312
  Chirality :  0.041   0.152    966
  Planarity :  0.004   0.054   1042
  Dihedral  :  9.756 110.892    898
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 27.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.32), residues: 722
  helix:  0.34 (0.28), residues: 346
  sheet: -1.27 (0.79), residues: 43
  loop : -0.63 (0.37), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 288 
 HIS   0.008   0.001   HIS A 585 
 PHE   0.014   0.001   PHE A 781 
 TYR   0.022   0.001   TYR A 414 
 ARG   0.005   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  244)
  hydrogen bonds       : angle       5.18705 (  705)
  covalent geometry    : bond        0.00291 ( 6367)
  covalent geometry    : angle       0.60855 ( 8643)

*********************** 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: 39
    poor density    : 172
  time to evaluate  : 0.621 
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  288 TRP cc_start: 0.7754 (t-100) cc_final: 0.7451 (t-100)
REVERT: A  292 LYS cc_start: 0.8496 (mttp) cc_final: 0.8218 (mttp)
REVERT: A  405 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7956 (p)
REVERT: A  428 GLU cc_start: 0.6805 (mp0) cc_final: 0.6520 (mp0)
REVERT: A  491 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8243 (m-80)
REVERT: A  531 ARG cc_start: 0.3396 (mmt180) cc_final: 0.2604 (tpt170)
REVERT: A  536 MET cc_start: 0.7226 (ptp) cc_final: 0.6912 (ptp)
REVERT: A  538 ILE cc_start: 0.8000 (mm) cc_final: 0.7667 (mp)
REVERT: A  539 ASP cc_start: 0.8034 (p0) cc_final: 0.7682 (p0)
REVERT: A  542 ILE cc_start: 0.8503 (mt) cc_final: 0.8280 (mt)
REVERT: A  545 LYS cc_start: 0.8504 (tttt) cc_final: 0.8157 (mttt)
REVERT: A  560 HIS cc_start: 0.7549 (t-90) cc_final: 0.6975 (t-90)
REVERT: A  578 LYS cc_start: 0.7767 (tttm) cc_final: 0.7467 (ttmm)
REVERT: A  597 ILE cc_start: 0.7721 (mp) cc_final: 0.7308 (mm)
REVERT: A  607 LYS cc_start: 0.7497 (pttm) cc_final: 0.6806 (pttm)
REVERT: A  617 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5869 (tp)
REVERT: A  651 PHE cc_start: 0.7393 (p90) cc_final: 0.6769 (p90)
REVERT: A  654 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7679 (mptt)
REVERT: A  666 LEU cc_start: 0.8717 (mm) cc_final: 0.8457 (mm)
REVERT: A  673 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6582 (tm-30)
REVERT: A  742 LEU cc_start: 0.8388 (tp) cc_final: 0.8116 (mp)
REVERT: A  746 ASN cc_start: 0.8001 (t0) cc_final: 0.7414 (p0)
REVERT: A  766 ILE cc_start: 0.7682 (pt) cc_final: 0.7317 (pt)
REVERT: A  772 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6451 (mm110)
REVERT: A  789 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7074 (pp)
REVERT: A  790 LYS cc_start: 0.8571 (ptpp) cc_final: 0.7927 (ptpp)
REVERT: A  793 LYS cc_start: 0.8968 (mttt) cc_final: 0.8428 (mttt)
REVERT: A  815 MET cc_start: 0.5463 (tmm) cc_final: 0.4646 (tmm)
REVERT: A  820 LYS cc_start: 0.8241 (tptt) cc_final: 0.7543 (tptt)
REVERT: A  823 TYR cc_start: 0.7881 (t80) cc_final: 0.7539 (t80)
REVERT: A  834 MET cc_start: 0.6924 (tmm) cc_final: 0.6509 (tmm)
REVERT: A  876 LYS cc_start: 0.7806 (tptt) cc_final: 0.7586 (tptt)
REVERT: A  880 LYS cc_start: 0.7546 (ttmm) cc_final: 0.7276 (mmtt)
REVERT: A  898 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6538 (tt0)
REVERT: A  939 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.6476 (t0)
REVERT: A  965 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7821 (mmtt)
REVERT: A 1002 MET cc_start: 0.6522 (mmm) cc_final: 0.6288 (mmm)
REVERT: A 1058 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7815 (ttmm)
  outliers start: 39
  outliers final: 22
  residues processed: 196
  average time/residue: 0.2158
  time to fit residues: 53.2208
Evaluate side-chains
  195 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
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  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  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  965 LYS
Chi-restraints excluded: chain A residue  977 LEU
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 8 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0270
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.9242

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** 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 = 0.4348 r_free = 0.4348 target = 0.161477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.135122 restraints weight = 11476.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.139880 restraints weight = 6488.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.143232 restraints weight = 4242.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6367  Z= 0.159
  Angle     :  0.655  10.154   8643  Z= 0.329
  Chirality :  0.043   0.156    966
  Planarity :  0.004   0.050   1042
  Dihedral  :  9.506  98.425    898
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 28.05 %
    Favored  : 65.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.32), residues: 722
  helix:  0.35 (0.28), residues: 350
  sheet: -1.40 (0.78), residues: 43
  loop : -0.68 (0.38), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 288 
 HIS   0.007   0.002   HIS A 585 
 PHE   0.014   0.001   PHE A 781 
 TYR   0.017   0.001   TYR A 414 
 ARG   0.005   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (  244)
  hydrogen bonds       : angle       5.09386 (  705)
  covalent geometry    : bond        0.00351 ( 6367)
  covalent geometry    : angle       0.65542 ( 8643)

*********************** 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
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 174
  time to evaluate  : 0.655 
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: 0.8245 (OUTLIER) cc_final: 0.8022 (p)
REVERT: A  428 GLU cc_start: 0.6823 (mp0) cc_final: 0.6620 (mp0)
REVERT: A  463 ASN cc_start: 0.7992 (m-40) cc_final: 0.7751 (m-40)
REVERT: A  491 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8185 (m-80)
REVERT: A  531 ARG cc_start: 0.3556 (mmt180) cc_final: 0.2818 (tpt170)
REVERT: A  536 MET cc_start: 0.7269 (ptp) cc_final: 0.6974 (ptp)
REVERT: A  539 ASP cc_start: 0.8040 (p0) cc_final: 0.7830 (p0)
REVERT: A  545 LYS cc_start: 0.8510 (tttt) cc_final: 0.8138 (mtpt)
REVERT: A  560 HIS cc_start: 0.7587 (t-90) cc_final: 0.7125 (t-90)
REVERT: A  578 LYS cc_start: 0.7834 (tttm) cc_final: 0.7433 (tttp)
REVERT: A  597 ILE cc_start: 0.7797 (mp) cc_final: 0.7349 (mm)
REVERT: A  617 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5945 (tp)
REVERT: A  651 PHE cc_start: 0.7394 (p90) cc_final: 0.6868 (p90)
REVERT: A  654 LYS cc_start: 0.7937 (mmtp) cc_final: 0.7572 (mptt)
REVERT: A  666 LEU cc_start: 0.8739 (mm) cc_final: 0.8491 (mm)
REVERT: A  672 LEU cc_start: 0.8327 (mm) cc_final: 0.7954 (mm)
REVERT: A  673 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6623 (tm-30)
REVERT: A  742 LEU cc_start: 0.8397 (tp) cc_final: 0.8119 (mp)
REVERT: A  789 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7107 (pp)
REVERT: A  790 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8112 (ptpp)
REVERT: A  793 LYS cc_start: 0.8993 (mttt) cc_final: 0.8472 (mttt)
REVERT: A  815 MET cc_start: 0.5501 (tmm) cc_final: 0.4671 (tmm)
REVERT: A  820 LYS cc_start: 0.8314 (tptt) cc_final: 0.7660 (tptt)
REVERT: A  823 TYR cc_start: 0.7879 (t80) cc_final: 0.7564 (t80)
REVERT: A  834 MET cc_start: 0.6828 (tmm) cc_final: 0.6434 (tmm)
REVERT: A  880 LYS cc_start: 0.7541 (ttmm) cc_final: 0.7334 (mmtt)
REVERT: A  919 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8149 (ttpt)
REVERT: A  932 LEU cc_start: 0.2161 (OUTLIER) cc_final: 0.0568 (mt)
REVERT: A  939 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.6547 (t0)
REVERT: A 1002 MET cc_start: 0.6644 (mmm) cc_final: 0.6375 (mmm)
REVERT: A 1059 GLN cc_start: 0.7620 (pt0) cc_final: 0.7401 (pp30)
  outliers start: 40
  outliers final: 21
  residues processed: 196
  average time/residue: 0.2054
  time to fit residues: 50.9822
Evaluate side-chains
  195 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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  516 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  617 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  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 48 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0070
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0970
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 669 ASN
** A 736 GLN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.161453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.134880 restraints weight = 11380.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.139655 restraints weight = 6468.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.143160 restraints weight = 4239.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.3462

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= 0.121
  Angle     :  0.640  10.435   8643  Z= 0.316
  Chirality :  0.042   0.269    966
  Planarity :  0.004   0.054   1042
  Dihedral  :  9.312  91.976    898
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 28.21 %
    Favored  : 66.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.33), residues: 722
  helix:  0.38 (0.28), residues: 356
  sheet: -1.34 (0.77), residues: 43
  loop : -0.58 (0.39), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 573 
 HIS   0.007   0.001   HIS A 585 
 PHE   0.014   0.001   PHE A 291 
 TYR   0.020   0.001   TYR A 414 
 ARG   0.005   0.000   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  244)
  hydrogen bonds       : angle       4.98012 (  705)
  covalent geometry    : bond        0.00283 ( 6367)
  covalent geometry    : angle       0.63969 ( 8643)

*********************** 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
  207 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.712 
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: 0.7587 (mp10) cc_final: 0.7224 (mp10)
REVERT: A  443 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7969 (tm-30)
REVERT: A  479 GLU cc_start: 0.7016 (tp30) cc_final: 0.6727 (tp30)
REVERT: A  491 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8093 (m-80)
REVERT: A  531 ARG cc_start: 0.3359 (mmt180) cc_final: 0.2527 (tpt170)
REVERT: A  536 MET cc_start: 0.7251 (ptp) cc_final: 0.6939 (ptp)
REVERT: A  560 HIS cc_start: 0.7551 (t-90) cc_final: 0.7022 (t70)
REVERT: A  578 LYS cc_start: 0.7799 (tttm) cc_final: 0.7340 (tttp)
REVERT: A  597 ILE cc_start: 0.7716 (mp) cc_final: 0.7391 (mm)
REVERT: A  607 LYS cc_start: 0.8471 (tptt) cc_final: 0.7989 (tppt)
REVERT: A  617 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6073 (tp)
REVERT: A  653 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7905 (mp)
REVERT: A  654 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7744 (mptt)
REVERT: A  666 LEU cc_start: 0.8659 (mm) cc_final: 0.8454 (mm)
REVERT: A  668 PHE cc_start: 0.8789 (t80) cc_final: 0.8557 (t80)
REVERT: A  672 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7846 (mm)
REVERT: A  673 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6584 (tm-30)
REVERT: A  705 ILE cc_start: 0.7311 (mt) cc_final: 0.6885 (pt)
REVERT: A  742 LEU cc_start: 0.8374 (tp) cc_final: 0.8093 (mp)
REVERT: A  772 GLN cc_start: 0.6925 (mm-40) cc_final: 0.6473 (mm110)
REVERT: A  790 LYS cc_start: 0.8564 (ptpp) cc_final: 0.8179 (ptpp)
REVERT: A  793 LYS cc_start: 0.8982 (mttt) cc_final: 0.8456 (mttt)
REVERT: A  804 CYS cc_start: 0.2388 (OUTLIER) cc_final: 0.0856 (p)
REVERT: A  815 MET cc_start: 0.5445 (tmm) cc_final: 0.4611 (tmm)
REVERT: A  820 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7623 (tptt)
REVERT: A  834 MET cc_start: 0.6787 (tmm) cc_final: 0.6387 (tmm)
REVERT: A  919 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8239 (tttt)
REVERT: A  932 LEU cc_start: 0.2051 (OUTLIER) cc_final: 0.0439 (mt)
REVERT: A  939 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.6192 (t0)
REVERT: A  956 TYR cc_start: 0.7743 (m-10) cc_final: 0.7394 (m-10)
REVERT: A 1002 MET cc_start: 0.6626 (mmm) cc_final: 0.6351 (mmm)
  outliers start: 37
  outliers final: 23
  residues processed: 188
  average time/residue: 0.2091
  time to fit residues: 49.8122
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  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 TRP
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  653 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  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 47 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0670
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** 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 = 0.4350 r_free = 0.4350 target = 0.162209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.135371 restraints weight = 11436.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.140236 restraints weight = 6466.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.143770 restraints weight = 4236.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.3648

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= 0.120
  Angle     :  0.643   9.713   8643  Z= 0.316
  Chirality :  0.042   0.248    966
  Planarity :  0.004   0.056   1042
  Dihedral  :  9.146  86.971    898
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 28.21 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.33), residues: 722
  helix:  0.47 (0.28), residues: 356
  sheet: -1.40 (0.77), residues: 43
  loop : -0.51 (0.39), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 888 
 HIS   0.008   0.001   HIS A 585 
 PHE   0.014   0.001   PHE A 291 
 TYR   0.015   0.001   TYR A 414 
 ARG   0.006   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  244)
  hydrogen bonds       : angle       4.88092 (  705)
  covalent geometry    : bond        0.00281 ( 6367)
  covalent geometry    : angle       0.64340 ( 8643)

*********************** 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
  204 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.683 
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: 0.7668 (mp10) cc_final: 0.7103 (mp10)
REVERT: A  443 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: A  479 GLU cc_start: 0.7027 (tp30) cc_final: 0.6796 (tp30)
REVERT: A  491 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8084 (m-80)
REVERT: A  531 ARG cc_start: 0.3164 (mmt180) cc_final: 0.2367 (tpt170)
REVERT: A  536 MET cc_start: 0.7271 (ptp) cc_final: 0.6959 (ptp)
REVERT: A  542 ILE cc_start: 0.8503 (mt) cc_final: 0.8226 (mt)
REVERT: A  560 HIS cc_start: 0.7528 (t-90) cc_final: 0.7262 (t70)
REVERT: A  578 LYS cc_start: 0.7795 (tttm) cc_final: 0.7553 (ttmm)
REVERT: A  597 ILE cc_start: 0.7716 (mp) cc_final: 0.7346 (mm)
REVERT: A  607 LYS cc_start: 0.8319 (tptt) cc_final: 0.7729 (ttpp)
REVERT: A  617 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6040 (tp)
REVERT: A  653 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7895 (mp)
REVERT: A  654 LYS cc_start: 0.7985 (mmtp) cc_final: 0.7754 (mptt)
REVERT: A  668 PHE cc_start: 0.8783 (t80) cc_final: 0.8535 (t80)
REVERT: A  672 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7792 (mm)
REVERT: A  673 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6687 (tm-30)
REVERT: A  705 ILE cc_start: 0.7384 (mt) cc_final: 0.6937 (pt)
REVERT: A  710 ASN cc_start: 0.7924 (t0) cc_final: 0.7721 (t0)
REVERT: A  742 LEU cc_start: 0.8392 (tp) cc_final: 0.8139 (mp)
REVERT: A  745 ASN cc_start: 0.8379 (p0) cc_final: 0.8107 (m110)
REVERT: A  746 ASN cc_start: 0.8158 (t0) cc_final: 0.7571 (p0)
REVERT: A  772 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6436 (mm110)
REVERT: A  790 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8106 (ptpp)
REVERT: A  793 LYS cc_start: 0.8979 (mttt) cc_final: 0.8466 (mttt)
REVERT: A  804 CYS cc_start: 0.2364 (OUTLIER) cc_final: 0.0793 (p)
REVERT: A  815 MET cc_start: 0.5427 (tmm) cc_final: 0.4587 (tmm)
REVERT: A  820 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7655 (tptt)
REVERT: A  834 MET cc_start: 0.6785 (tmm) cc_final: 0.6358 (tmm)
REVERT: A  919 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8159 (ttpt)
REVERT: A  932 LEU cc_start: 0.2052 (OUTLIER) cc_final: 0.0422 (mt)
REVERT: A  939 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6213 (t0)
REVERT: A 1002 MET cc_start: 0.6621 (mmm) cc_final: 0.6340 (mmm)
REVERT: A 1058 LYS cc_start: 0.8094 (tppt) cc_final: 0.7651 (mttp)
  outliers start: 34
  outliers final: 21
  residues processed: 188
  average time/residue: 0.2030
  time to fit residues: 48.4730
Evaluate side-chains
  195 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 TRP
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  653 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  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0570
   chunk 68 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.9704

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 784 ASN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.159563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.132866 restraints weight = 11341.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.137555 restraints weight = 6488.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.140998 restraints weight = 4283.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6611
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6367  Z= 0.162
  Angle     :  0.682  10.382   8643  Z= 0.338
  Chirality :  0.044   0.247    966
  Planarity :  0.004   0.051   1042
  Dihedral  :  9.161  84.228    898
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.33), residues: 722
  helix:  0.20 (0.27), residues: 365
  sheet: -1.50 (0.76), residues: 43
  loop : -0.50 (0.40), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 888 
 HIS   0.005   0.001   HIS A 585 
 PHE   0.013   0.002   PHE A 759 
 TYR   0.014   0.001   TYR A 743 
 ARG   0.008   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  244)
  hydrogen bonds       : angle       4.92721 (  705)
  covalent geometry    : bond        0.00358 ( 6367)
  covalent geometry    : angle       0.68195 ( 8643)

*********************** 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
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 181
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7775 (mp10) cc_final: 0.7410 (mp10)
REVERT: A  447 GLU cc_start: 0.8494 (tt0) cc_final: 0.7855 (tm-30)
REVERT: A  479 GLU cc_start: 0.7098 (tp30) cc_final: 0.6544 (tp30)
REVERT: A  523 ASP cc_start: 0.7762 (p0) cc_final: 0.7466 (p0)
REVERT: A  536 MET cc_start: 0.7306 (ptp) cc_final: 0.7014 (ptp)
REVERT: A  542 ILE cc_start: 0.8532 (mt) cc_final: 0.8283 (mt)
REVERT: A  560 HIS cc_start: 0.7578 (t-90) cc_final: 0.7331 (t70)
REVERT: A  597 ILE cc_start: 0.7762 (mp) cc_final: 0.7504 (mp)
REVERT: A  617 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6101 (tp)
REVERT: A  653 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7946 (mp)
REVERT: A  654 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7745 (mptt)
REVERT: A  668 PHE cc_start: 0.8797 (t80) cc_final: 0.8529 (t80)
REVERT: A  672 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7846 (mm)
REVERT: A  673 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6728 (tm-30)
REVERT: A  705 ILE cc_start: 0.7556 (mt) cc_final: 0.7104 (pt)
REVERT: A  710 ASN cc_start: 0.7938 (t0) cc_final: 0.7696 (t0)
REVERT: A  742 LEU cc_start: 0.8406 (tp) cc_final: 0.8179 (mp)
REVERT: A  745 ASN cc_start: 0.8377 (p0) cc_final: 0.8145 (m110)
REVERT: A  746 ASN cc_start: 0.8124 (t0) cc_final: 0.7497 (p0)
REVERT: A  772 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6542 (mm110)
REVERT: A  789 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7068 (pp)
REVERT: A  790 LYS cc_start: 0.8577 (ptpp) cc_final: 0.8172 (ptpp)
REVERT: A  793 LYS cc_start: 0.8998 (mttt) cc_final: 0.8484 (mttt)
REVERT: A  804 CYS cc_start: 0.2331 (OUTLIER) cc_final: 0.0729 (p)
REVERT: A  815 MET cc_start: 0.5441 (tmm) cc_final: 0.4607 (tmm)
REVERT: A  820 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7689 (tptt)
REVERT: A  834 MET cc_start: 0.6848 (tmm) cc_final: 0.6402 (tmm)
REVERT: A  880 LYS cc_start: 0.7377 (ttmm) cc_final: 0.7041 (mmtt)
REVERT: A  883 VAL cc_start: 0.8769 (t) cc_final: 0.8287 (p)
REVERT: A  919 LYS cc_start: 0.8597 (tmtt) cc_final: 0.8185 (ttpt)
REVERT: A  932 LEU cc_start: 0.2063 (OUTLIER) cc_final: 0.0479 (mt)
REVERT: A  939 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.6092 (t0)
REVERT: A 1002 MET cc_start: 0.6661 (mmm) cc_final: 0.6378 (mmm)
REVERT: A 1058 LYS cc_start: 0.8102 (tppt) cc_final: 0.7711 (mttt)
  outliers start: 33
  outliers final: 22
  residues processed: 197
  average time/residue: 0.2047
  time to fit residues: 51.7404
Evaluate side-chains
  207 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 177
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  653 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  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** 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 = 0.4366 r_free = 0.4366 target = 0.163262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.135502 restraints weight = 11586.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.140456 restraints weight = 6437.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.144053 restraints weight = 4197.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.4126

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= 0.153
  Angle     :  0.697   9.828   8643  Z= 0.347
  Chirality :  0.044   0.241    966
  Planarity :  0.005   0.052   1042
  Dihedral  :  9.141  84.443    898
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 30.02 %
    Favored  : 65.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.33), residues: 722
  helix:  0.17 (0.27), residues: 365
  sheet: -1.42 (0.77), residues: 43
  loop : -0.48 (0.40), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 888 
 HIS   0.004   0.001   HIS A 585 
 PHE   0.017   0.001   PHE A 291 
 TYR   0.022   0.001   TYR A 879 
 ARG   0.007   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  244)
  hydrogen bonds       : angle       4.92669 (  705)
  covalent geometry    : bond        0.00344 ( 6367)
  covalent geometry    : angle       0.69724 ( 8643)

*********************** 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
  216 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7743 (mp10) cc_final: 0.7115 (mp10)
REVERT: A  447 GLU cc_start: 0.8607 (tt0) cc_final: 0.7990 (tm-30)
REVERT: A  479 GLU cc_start: 0.7098 (tp30) cc_final: 0.6830 (tp30)
REVERT: A  491 PHE cc_start: 0.8468 (m-10) cc_final: 0.8248 (m-80)
REVERT: A  523 ASP cc_start: 0.7769 (p0) cc_final: 0.7468 (p0)
REVERT: A  536 MET cc_start: 0.7267 (ptp) cc_final: 0.6946 (ptp)
REVERT: A  542 ILE cc_start: 0.8509 (mt) cc_final: 0.8266 (mt)
REVERT: A  560 HIS cc_start: 0.7656 (t-90) cc_final: 0.7267 (t70)
REVERT: A  578 LYS cc_start: 0.7825 (tttm) cc_final: 0.7382 (tttp)
REVERT: A  597 ILE cc_start: 0.7683 (mp) cc_final: 0.7452 (mp)
REVERT: A  617 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5862 (tp)
REVERT: A  651 PHE cc_start: 0.7360 (p90) cc_final: 0.6763 (p90)
REVERT: A  653 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7898 (mp)
REVERT: A  654 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7692 (mptt)
REVERT: A  668 PHE cc_start: 0.8789 (t80) cc_final: 0.8554 (t80)
REVERT: A  672 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7897 (mm)
REVERT: A  673 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6923 (tm-30)
REVERT: A  705 ILE cc_start: 0.7428 (mt) cc_final: 0.7019 (pt)
REVERT: A  710 ASN cc_start: 0.7846 (t0) cc_final: 0.7575 (t0)
REVERT: A  742 LEU cc_start: 0.8480 (tp) cc_final: 0.8234 (mp)
REVERT: A  745 ASN cc_start: 0.8369 (p0) cc_final: 0.8137 (m110)
REVERT: A  746 ASN cc_start: 0.8072 (t0) cc_final: 0.7465 (p0)
REVERT: A  772 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6576 (mm110)
REVERT: A  790 LYS cc_start: 0.8669 (ptpp) cc_final: 0.8367 (ptpp)
REVERT: A  793 LYS cc_start: 0.9028 (mttt) cc_final: 0.8498 (mttt)
REVERT: A  804 CYS cc_start: 0.2460 (OUTLIER) cc_final: 0.0924 (p)
REVERT: A  815 MET cc_start: 0.5593 (tmm) cc_final: 0.4754 (tmm)
REVERT: A  820 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7766 (tptt)
REVERT: A  834 MET cc_start: 0.6948 (tmm) cc_final: 0.6467 (tmm)
REVERT: A  876 LYS cc_start: 0.7931 (tptt) cc_final: 0.7517 (tptt)
REVERT: A  883 VAL cc_start: 0.8733 (t) cc_final: 0.8299 (p)
REVERT: A  919 LYS cc_start: 0.8532 (tmtt) cc_final: 0.8088 (ttpt)
REVERT: A  932 LEU cc_start: 0.2007 (OUTLIER) cc_final: 0.0534 (mt)
REVERT: A  939 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6239 (m-40)
REVERT: A  965 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7677 (mmtt)
REVERT: A  975 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7696 (mmtm)
REVERT: A 1002 MET cc_start: 0.6803 (mmm) cc_final: 0.6513 (mmm)
REVERT: A 1028 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7645 (tpp80)
REVERT: A 1040 PHE cc_start: 0.7629 (m-80) cc_final: 0.7415 (m-80)
  outliers start: 32
  outliers final: 22
  residues processed: 197
  average time/residue: 0.2053
  time to fit residues: 51.9034
Evaluate side-chains
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 TRP
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  666 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  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 70 optimal weight:    0.2980
   chunk 40 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 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 = 0.4316 r_free = 0.4316 target = 0.159728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.133118 restraints weight = 11520.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.137820 restraints weight = 6550.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.141167 restraints weight = 4318.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6596
moved from start:          0.4286

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= 0.148
  Angle     :  0.718  10.232   8643  Z= 0.358
  Chirality :  0.045   0.235    966
  Planarity :  0.005   0.053   1042
  Dihedral  :  9.103  84.540    898
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 29.86 %
    Favored  : 64.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.33), residues: 722
  helix:  0.18 (0.28), residues: 365
  sheet: -1.31 (0.77), residues: 43
  loop : -0.45 (0.41), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 888 
 HIS   0.004   0.001   HIS A 585 
 PHE   0.020   0.002   PHE A 291 
 TYR   0.022   0.002   TYR A 879 
 ARG   0.007   0.001   ARG A 680 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  244)
  hydrogen bonds       : angle       4.96193 (  705)
  covalent geometry    : bond        0.00339 ( 6367)
  covalent geometry    : angle       0.71800 ( 8643)

********************** 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
  212 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 177
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7727 (mp10) cc_final: 0.7445 (mp10)
REVERT: A  447 GLU cc_start: 0.8450 (tt0) cc_final: 0.7838 (tm-30)
REVERT: A  479 GLU cc_start: 0.7095 (tp30) cc_final: 0.6848 (tp30)
REVERT: A  491 PHE cc_start: 0.8323 (m-10) cc_final: 0.8100 (m-80)
REVERT: A  523 ASP cc_start: 0.7773 (p0) cc_final: 0.7460 (p0)
REVERT: A  536 MET cc_start: 0.7260 (ptp) cc_final: 0.6977 (ptp)
REVERT: A  542 ILE cc_start: 0.8509 (mt) cc_final: 0.8269 (mt)
REVERT: A  560 HIS cc_start: 0.7551 (t-90) cc_final: 0.7320 (t70)
REVERT: A  597 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7536 (mp)
REVERT: A  617 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6071 (tp)
REVERT: A  651 PHE cc_start: 0.7276 (p90) cc_final: 0.6762 (p90)
REVERT: A  654 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7750 (mptt)
REVERT: A  668 PHE cc_start: 0.8747 (t80) cc_final: 0.8495 (t80)
REVERT: A  672 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7895 (mm)
REVERT: A  673 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6750 (tm-30)
REVERT: A  705 ILE cc_start: 0.7503 (mt) cc_final: 0.7070 (pt)
REVERT: A  710 ASN cc_start: 0.7886 (t0) cc_final: 0.7598 (t0)
REVERT: A  742 LEU cc_start: 0.8434 (tp) cc_final: 0.8196 (mp)
REVERT: A  746 ASN cc_start: 0.8180 (t0) cc_final: 0.7569 (p0)
REVERT: A  772 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6574 (mm-40)
REVERT: A  789 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7038 (pp)
REVERT: A  790 LYS cc_start: 0.8558 (ptpp) cc_final: 0.8219 (ptpp)
REVERT: A  793 LYS cc_start: 0.8990 (mttt) cc_final: 0.8498 (mttt)
REVERT: A  804 CYS cc_start: 0.2403 (OUTLIER) cc_final: 0.0825 (p)
REVERT: A  815 MET cc_start: 0.5426 (tmm) cc_final: 0.4610 (tmm)
REVERT: A  820 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7697 (tptt)
REVERT: A  834 MET cc_start: 0.6811 (tmm) cc_final: 0.6313 (tmm)
REVERT: A  876 LYS cc_start: 0.7877 (tptt) cc_final: 0.7475 (tptt)
REVERT: A  883 VAL cc_start: 0.8777 (t) cc_final: 0.8318 (p)
REVERT: A  888 TRP cc_start: 0.7956 (t60) cc_final: 0.6707 (t60)
REVERT: A  919 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8184 (ttpt)
REVERT: A  932 LEU cc_start: 0.1931 (OUTLIER) cc_final: 0.0379 (mt)
REVERT: A  939 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6257 (m-40)
REVERT: A  965 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7651 (mmtt)
REVERT: A  986 GLN cc_start: 0.8568 (pp30) cc_final: 0.8341 (pp30)
REVERT: A 1002 MET cc_start: 0.6748 (mmm) cc_final: 0.6467 (mmm)
REVERT: A 1028 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7442 (tpp80)
REVERT: A 1040 PHE cc_start: 0.7536 (m-80) cc_final: 0.7308 (m-80)
REVERT: A 1058 LYS cc_start: 0.8076 (tppt) cc_final: 0.7672 (mttp)
  outliers start: 35
  outliers final: 25
  residues processed: 191
  average time/residue: 0.2032
  time to fit residues: 49.6715
Evaluate side-chains
  207 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 TRP
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  698 SER
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  894 ARG
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0020
   chunk 18 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 20 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 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 = 0.4331 r_free = 0.4331 target = 0.161096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.134894 restraints weight = 11405.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.139595 restraints weight = 6410.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.142983 restraints weight = 4182.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.4378

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= 0.137
  Angle     :  0.722  10.191   8643  Z= 0.360
  Chirality :  0.044   0.227    966
  Planarity :  0.005   0.054   1042
  Dihedral  :  9.017  84.447    898
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.33), residues: 722
  helix:  0.31 (0.28), residues: 359
  sheet: -1.30 (0.78), residues: 43
  loop : -0.43 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 888 
 HIS   0.003   0.001   HIS A 585 
 PHE   0.017   0.001   PHE A 291 
 TYR   0.022   0.001   TYR A 879 
 ARG   0.007   0.001   ARG A 631 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  244)
  hydrogen bonds       : angle       4.90528 (  705)
  covalent geometry    : bond        0.00317 ( 6367)
  covalent geometry    : angle       0.72203 ( 8643)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3264.09 seconds
wall clock time: 57 minutes 31.07 seconds (3451.07 seconds total)