Starting phenix.real_space_refine
on Tue Mar 11 16:06:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxu_40859/03_2025/8sxu_40859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxu_40859/03_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_40859/03_2025/8sxu_40859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxu_40859/03_2025/8sxu_40859.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxu_40859/03_2025/8sxu_40859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxu_40859/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.09, per 1000 atoms: 0.66
  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: 1.44
  Conformation dependent library (CDL) restraints added in 904.7 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: 2.10
  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: 1.89

  Time building geometry restraints manager: 1.72 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:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.850
  Find NCS groups from input model:        0.060
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.820
-------------------------------------------------------------------------------
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= 0.164
  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 

*********************** 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  : 0.750 
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: 0.2264
  time to fit residues: 49.8230
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  : 0.671 
-------------------------------------------------------------------------------
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 = 0.138911 restraints weight = 11486.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.143617 restraints weight = 6684.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.146840 restraints weight = 4499.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
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= 0.189
  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 

*********************** 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  : 0.681 
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: 0.8182 (mttt)
REVERT: A  547 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7634 (mt)
REVERT: A  552 GLN cc_start: 0.7160 (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: 0.6919 (mt)
REVERT: A  651 PHE cc_start: 0.7285 (p90) cc_final: 0.6572 (p90)
REVERT: A  654 LYS cc_start: 0.7938 (mmtp) cc_final: 0.7684 (mptt)
REVERT: A  663 LEU cc_start: 0.8323 (tp) cc_final: 0.8076 (pt)
REVERT: A  666 LEU cc_start: 0.8686 (mm) cc_final: 0.8437 (mm)
REVERT: A  673 GLU cc_start: 0.7124 (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: 0.8789 (mtmm) cc_final: 0.8488 (mtmm)
REVERT: A  759 PHE cc_start: 0.7004 (m-80) cc_final: 0.6226 (m-80)
REVERT: A  766 ILE cc_start: 0.7745 (pt) cc_final: 0.7447 (pt)
REVERT: A  772 GLN cc_start: 0.6640 (mm-40) cc_final: 0.6404 (mm-40)
REVERT: A  789 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.6895 (pp)
REVERT: A  790 LYS cc_start: 0.8524 (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: 0.5324 (tmm) cc_final: 0.4533 (tmm)
REVERT: A  823 TYR cc_start: 0.7536 (t80) cc_final: 0.7268 (t80)
REVERT: A  834 MET cc_start: 0.6928 (tmm) cc_final: 0.6613 (tmm)
REVERT: A  837 PHE cc_start: 0.7688 (m-80) cc_final: 0.7453 (m-80)
REVERT: A  876 LYS cc_start: 0.7638 (tptt) cc_final: 0.7359 (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: 0.8323 (ttmm) cc_final: 0.8097 (ttmm)
  outliers start: 33
  outliers final: 20
  residues processed: 189
  average time/residue: 0.2108
  time to fit residues: 50.5160
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  : 0.713 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 669 ASN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.158923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.133212 restraints weight = 11629.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.137869 restraints weight = 6524.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.141182 restraints weight = 4259.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6367  Z= 0.306
  Angle     :  0.697   8.023   8643  Z= 0.366
  Chirality :  0.045   0.171    966
  Planarity :  0.005   0.043   1042
  Dihedral  : 10.067 112.826    898
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 26.09 %
    Favored  : 67.27 %
  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: -0.80 (0.32), residues: 722
  helix: -0.04 (0.27), residues: 367
  sheet: -1.43 (0.80), residues: 43
  loop : -0.86 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 573 
 HIS   0.003   0.001   HIS A 585 
 PHE   0.016   0.002   PHE A 781 
 TYR   0.013   0.002   TYR A 768 
 ARG   0.009   0.001   ARG A 747 

*********************** 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
  210 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 166
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7550 (mp10) cc_final: 0.7334 (mp10)
REVERT: A  405 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8069 (p)
REVERT: A  463 ASN cc_start: 0.8051 (m-40) cc_final: 0.7841 (m110)
REVERT: A  491 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8325 (m-80)
REVERT: A  531 ARG cc_start: 0.3681 (mmt180) cc_final: 0.2964 (tpt170)
REVERT: A  536 MET cc_start: 0.7290 (ptp) cc_final: 0.6963 (ptp)
REVERT: A  560 HIS cc_start: 0.7598 (t-90) cc_final: 0.6879 (t-90)
REVERT: A  597 ILE cc_start: 0.7873 (mp) cc_final: 0.7352 (mm)
REVERT: A  607 LYS cc_start: 0.7528 (pttm) cc_final: 0.6876 (pttm)
REVERT: A  617 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5814 (mt)
REVERT: A  651 PHE cc_start: 0.7478 (p90) cc_final: 0.6891 (p90)
REVERT: A  654 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7735 (mptt)
REVERT: A  663 LEU cc_start: 0.8505 (tp) cc_final: 0.8277 (tp)
REVERT: A  666 LEU cc_start: 0.8838 (mm) cc_final: 0.8429 (mm)
REVERT: A  672 LEU cc_start: 0.8458 (mm) cc_final: 0.8159 (mm)
REVERT: A  673 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: A  746 ASN cc_start: 0.8113 (t0) cc_final: 0.7558 (p0)
REVERT: A  759 PHE cc_start: 0.7537 (m-80) cc_final: 0.6974 (m-80)
REVERT: A  772 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6617 (mm110)
REVERT: A  789 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7125 (pp)
REVERT: A  790 LYS cc_start: 0.8638 (ptpp) cc_final: 0.7996 (ptpp)
REVERT: A  793 LYS cc_start: 0.8992 (mttt) cc_final: 0.8458 (mttt)
REVERT: A  815 MET cc_start: 0.5506 (tmm) cc_final: 0.4707 (tmm)
REVERT: A  822 ILE cc_start: 0.8278 (mm) cc_final: 0.7933 (mm)
REVERT: A  823 TYR cc_start: 0.7844 (t80) cc_final: 0.7613 (t80)
REVERT: A  834 MET cc_start: 0.6976 (tmm) cc_final: 0.6620 (tmm)
REVERT: A  883 VAL cc_start: 0.8814 (t) cc_final: 0.8320 (p)
REVERT: A  898 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7103 (tm-30)
REVERT: A  919 LYS cc_start: 0.8595 (tmtt) cc_final: 0.8152 (ttpt)
REVERT: A  939 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.6525 (m-40)
REVERT: A  986 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: A 1002 MET cc_start: 0.6606 (mmm) cc_final: 0.6384 (mmm)
  outliers start: 44
  outliers final: 23
  residues processed: 192
  average time/residue: 0.2255
  time to fit residues: 55.3352
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  : 0.712 
-------------------------------------------------------------------------------
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  423 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  546 ILE
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  619 LYS
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1031 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.159604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.133619 restraints weight = 11635.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.138352 restraints weight = 6578.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.141731 restraints weight = 4301.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6367  Z= 0.195
  Angle     :  0.623   9.272   8643  Z= 0.315
  Chirality :  0.042   0.155    966
  Planarity :  0.004   0.047   1042
  Dihedral  :  9.716 104.095    898
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 27.75 %
    Favored  : 67.12 %
  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 (0.32), residues: 722
  helix:  0.37 (0.28), residues: 353
  sheet: -1.41 (0.78), residues: 43
  loop : -0.74 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 288 
 HIS   0.010   0.001   HIS A 585 
 PHE   0.016   0.002   PHE A 781 
 TYR   0.009   0.001   TYR A 879 
 ARG   0.005   0.000   ARG A 747 

*********************** 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
  208 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8055 (p)
REVERT: A  463 ASN cc_start: 0.7990 (m-40) cc_final: 0.7764 (m-40)
REVERT: A  479 GLU cc_start: 0.7099 (tp30) cc_final: 0.6766 (tp30)
REVERT: A  491 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8225 (m-80)
REVERT: A  531 ARG cc_start: 0.3581 (mmt180) cc_final: 0.2772 (tpt170)
REVERT: A  536 MET cc_start: 0.7261 (ptp) cc_final: 0.6963 (ptp)
REVERT: A  560 HIS cc_start: 0.7648 (t-90) cc_final: 0.7057 (t-90)
REVERT: A  578 LYS cc_start: 0.7811 (tttm) cc_final: 0.7365 (tttp)
REVERT: A  597 ILE cc_start: 0.7839 (mp) cc_final: 0.7485 (mm)
REVERT: A  654 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7704 (mptt)
REVERT: A  666 LEU cc_start: 0.8595 (mm) cc_final: 0.8347 (mm)
REVERT: A  672 LEU cc_start: 0.8307 (mm) cc_final: 0.8044 (mm)
REVERT: A  673 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6584 (tm-30)
REVERT: A  705 ILE cc_start: 0.7429 (mt) cc_final: 0.6760 (pt)
REVERT: A  720 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8481 (mtmm)
REVERT: A  742 LEU cc_start: 0.8355 (tp) cc_final: 0.8074 (mp)
REVERT: A  789 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7108 (pp)
REVERT: A  790 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8073 (ptpp)
REVERT: A  793 LYS cc_start: 0.8980 (mttt) cc_final: 0.8446 (mttt)
REVERT: A  815 MET cc_start: 0.5545 (tmm) cc_final: 0.4731 (tmm)
REVERT: A  820 LYS cc_start: 0.8292 (tptt) cc_final: 0.7611 (tptt)
REVERT: A  823 TYR cc_start: 0.7871 (t80) cc_final: 0.7521 (t80)
REVERT: A  834 MET cc_start: 0.6929 (tmm) cc_final: 0.6544 (tmm)
REVERT: A  880 LYS cc_start: 0.7488 (ttmm) cc_final: 0.7265 (mmtt)
REVERT: A  890 TRP cc_start: 0.6920 (OUTLIER) cc_final: 0.6550 (m100)
REVERT: A  919 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8148 (ttpt)
REVERT: A  939 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6377 (m-40)
REVERT: A  949 LEU cc_start: 0.7448 (tt) cc_final: 0.6518 (mt)
REVERT: A 1002 MET cc_start: 0.6586 (mmm) cc_final: 0.6310 (mmm)
  outliers start: 34
  outliers final: 21
  residues processed: 193
  average time/residue: 0.2144
  time to fit residues: 52.6939
Evaluate side-chains
  191 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  674 VAL
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  890 TRP
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0370
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 898 GLN
** 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 = 0.4366 r_free = 0.4366 target = 0.162832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.136398 restraints weight = 11528.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.141325 restraints weight = 6295.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.144872 restraints weight = 4035.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6367  Z= 0.193
  Angle     :  0.620   9.254   8643  Z= 0.312
  Chirality :  0.043   0.285    966
  Planarity :  0.004   0.052   1042
  Dihedral  :  9.518  98.342    898
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 27.90 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.41 (0.28), residues: 353
  sheet: -1.45 (0.77), residues: 43
  loop : -0.70 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 890 
 HIS   0.009   0.001   HIS A 585 
 PHE   0.011   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 634 
 ARG   0.003   0.000   ARG A 747 

*********************** 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
  213 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.734 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8063 (p)
REVERT: A  428 GLU cc_start: 0.7005 (mp0) cc_final: 0.6718 (mp0)
REVERT: A  463 ASN cc_start: 0.8038 (m-40) cc_final: 0.7802 (m-40)
REVERT: A  479 GLU cc_start: 0.7140 (tp30) cc_final: 0.6810 (tp30)
REVERT: A  491 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8201 (m-80)
REVERT: A  531 ARG cc_start: 0.3150 (mmt180) cc_final: 0.2553 (tpt170)
REVERT: A  536 MET cc_start: 0.7215 (ptp) cc_final: 0.6861 (ptp)
REVERT: A  560 HIS cc_start: 0.7640 (t-90) cc_final: 0.7202 (t70)
REVERT: A  578 LYS cc_start: 0.7828 (tttm) cc_final: 0.7426 (tttp)
REVERT: A  597 ILE cc_start: 0.7739 (mp) cc_final: 0.7359 (mm)
REVERT: A  617 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5719 (mt)
REVERT: A  654 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7627 (mptt)
REVERT: A  666 LEU cc_start: 0.8626 (mm) cc_final: 0.8422 (mm)
REVERT: A  672 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7990 (mm)
REVERT: A  673 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6781 (tm-30)
REVERT: A  705 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6591 (pt)
REVERT: A  710 ASN cc_start: 0.7953 (t0) cc_final: 0.7723 (t0)
REVERT: A  742 LEU cc_start: 0.8380 (tp) cc_final: 0.8061 (mp)
REVERT: A  789 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7225 (pp)
REVERT: A  790 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8247 (ptpp)
REVERT: A  793 LYS cc_start: 0.9011 (mttt) cc_final: 0.8470 (mttt)
REVERT: A  815 MET cc_start: 0.5668 (tmm) cc_final: 0.4834 (tmm)
REVERT: A  820 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7734 (tptt)
REVERT: A  834 MET cc_start: 0.7034 (tmm) cc_final: 0.6681 (tmm)
REVERT: A  888 TRP cc_start: 0.7871 (t60) cc_final: 0.6290 (t60)
REVERT: A  919 LYS cc_start: 0.8501 (tmtt) cc_final: 0.8052 (ttpt)
REVERT: A  939 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.6132 (t0)
REVERT: A  949 LEU cc_start: 0.7524 (tt) cc_final: 0.6546 (mt)
REVERT: A  956 TYR cc_start: 0.7785 (m-10) cc_final: 0.7531 (m-10)
REVERT: A 1002 MET cc_start: 0.6691 (mmm) cc_final: 0.6407 (mmm)
REVERT: A 1046 ASP cc_start: 0.7141 (p0) cc_final: 0.6883 (p0)
REVERT: A 1059 GLN cc_start: 0.7082 (pp30) cc_final: 0.6807 (pp30)
  outliers start: 37
  outliers final: 25
  residues processed: 195
  average time/residue: 0.2241
  time to fit residues: 55.6988
Evaluate side-chains
  198 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 165
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
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  291 PHE
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  546 ILE
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  619 LYS
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  705 ILE
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  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0030
   chunk 66 optimal weight:    0.1980
   chunk 6 optimal weight:    5.9990
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 47 optimal weight:    0.1980
   overall best weight:    0.2790

-------------------------------------------------------------------------------
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 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 = 0.4349 r_free = 0.4349 target = 0.162035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.135744 restraints weight = 11333.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.140560 restraints weight = 6396.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.144096 restraints weight = 4182.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.3496

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= 0.173
  Angle     :  0.611   8.577   8643  Z= 0.305
  Chirality :  0.042   0.249    966
  Planarity :  0.004   0.055   1042
  Dihedral  :  9.273  91.150    898
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 29.26 %
    Favored  : 65.76 %
  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: -0.24 (0.33), residues: 722
  helix:  0.52 (0.28), residues: 353
  sheet: -1.49 (0.76), residues: 43
  loop : -0.62 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 890 
 HIS   0.008   0.001   HIS A 585 
 PHE   0.015   0.001   PHE A 291 
 TYR   0.018   0.001   TYR A 414 
 ARG   0.004   0.000   ARG A 747 

*********************** 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: 33
    poor density    : 174
  time to evaluate  : 0.727 
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: symmetry clash
REVERT: A  285 GLN cc_start: 0.7487 (mp10) cc_final: 0.7275 (mp10)
REVERT: A  428 GLU cc_start: 0.6849 (mp0) cc_final: 0.6606 (mp0)
REVERT: A  443 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: A  479 GLU cc_start: 0.7122 (tp30) cc_final: 0.6755 (tp30)
REVERT: A  491 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8109 (m-80)
REVERT: A  523 ASP cc_start: 0.7715 (p0) cc_final: 0.7385 (p0)
REVERT: A  531 ARG cc_start: 0.2919 (mmt180) cc_final: 0.2253 (ttt180)
REVERT: A  536 MET cc_start: 0.7252 (ptp) cc_final: 0.6949 (ptp)
REVERT: A  542 ILE cc_start: 0.8483 (mt) cc_final: 0.8260 (mt)
REVERT: A  560 HIS cc_start: 0.7596 (t-90) cc_final: 0.7299 (t70)
REVERT: A  578 LYS cc_start: 0.7797 (tttm) cc_final: 0.7400 (tttp)
REVERT: A  597 ILE cc_start: 0.7756 (mp) cc_final: 0.7378 (mm)
REVERT: A  607 LYS cc_start: 0.7538 (pttm) cc_final: 0.6838 (ttpt)
REVERT: A  617 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5777 (tp)
REVERT: A  654 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7708 (mptt)
REVERT: A  666 LEU cc_start: 0.8543 (mm) cc_final: 0.8327 (mm)
REVERT: A  672 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7893 (mm)
REVERT: A  673 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6686 (tm-30)
REVERT: A  705 ILE cc_start: 0.7444 (mt) cc_final: 0.6853 (pt)
REVERT: A  710 ASN cc_start: 0.7925 (t0) cc_final: 0.7707 (t0)
REVERT: A  742 LEU cc_start: 0.8384 (tp) cc_final: 0.8085 (mp)
REVERT: A  766 ILE cc_start: 0.7576 (pt) cc_final: 0.6661 (mt)
REVERT: A  772 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6499 (mm110)
REVERT: A  790 LYS cc_start: 0.8589 (ptpp) cc_final: 0.8242 (ptpp)
REVERT: A  793 LYS cc_start: 0.8994 (mttt) cc_final: 0.8458 (mttt)
REVERT: A  804 CYS cc_start: 0.2424 (OUTLIER) cc_final: 0.0896 (p)
REVERT: A  815 MET cc_start: 0.5463 (tmm) cc_final: 0.4641 (tmm)
REVERT: A  820 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7673 (tptt)
REVERT: A  834 MET cc_start: 0.6871 (tmm) cc_final: 0.6500 (tmm)
REVERT: A  888 TRP cc_start: 0.7886 (t60) cc_final: 0.6412 (t60)
REVERT: A  890 TRP cc_start: 0.6880 (OUTLIER) cc_final: 0.6530 (m100)
REVERT: A  919 LYS cc_start: 0.8559 (tmtt) cc_final: 0.8131 (ttpt)
REVERT: A  939 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6118 (t0)
REVERT: A  949 LEU cc_start: 0.7442 (tt) cc_final: 0.6576 (mt)
REVERT: A  956 TYR cc_start: 0.7762 (m-10) cc_final: 0.7441 (m-10)
REVERT: A  997 LYS cc_start: 0.8427 (tmtt) cc_final: 0.7636 (mtmt)
REVERT: A 1002 MET cc_start: 0.6643 (mmm) cc_final: 0.6359 (mmm)
REVERT: A 1046 ASP cc_start: 0.7206 (p0) cc_final: 0.6901 (p0)
REVERT: A 1047 LYS cc_start: 0.7858 (tttt) cc_final: 0.7552 (tttp)
  outliers start: 33
  outliers final: 22
  residues processed: 189
  average time/residue: 0.2199
  time to fit residues: 52.5307
Evaluate side-chains
  198 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 169
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  535 LEU
Chi-restraints excluded: chain A residue  538 ILE
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  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
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  890 TRP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0670
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.5320

-------------------------------------------------------------------------------
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 552 GLN
** A 669 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 = 0.4377 r_free = 0.4377 target = 0.164065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.137362 restraints weight = 11487.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.142389 restraints weight = 6280.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.145984 restraints weight = 4011.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6367  Z= 0.192
  Angle     :  0.630   7.877   8643  Z= 0.317
  Chirality :  0.042   0.239    966
  Planarity :  0.004   0.054   1042
  Dihedral  :  9.107  85.395    898
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 30.47 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.25 (0.33), residues: 722
  helix:  0.42 (0.28), residues: 352
  sheet: -1.45 (0.77), residues: 43
  loop : -0.52 (0.39), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 888 
 HIS   0.007   0.001   HIS A 585 
 PHE   0.011   0.001   PHE A 291 
 TYR   0.019   0.001   TYR A 414 
 ARG   0.004   0.000   ARG A 747 

*********************** 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
  193 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.761 
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: symmetry clash
REVERT: A  479 GLU cc_start: 0.7115 (tp30) cc_final: 0.6722 (tp30)
REVERT: A  491 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8173 (m-80)
REVERT: A  536 MET cc_start: 0.7271 (ptp) cc_final: 0.6925 (ptp)
REVERT: A  542 ILE cc_start: 0.8486 (mt) cc_final: 0.8248 (mt)
REVERT: A  560 HIS cc_start: 0.7648 (t-90) cc_final: 0.7272 (t70)
REVERT: A  573 TRP cc_start: 0.8014 (p-90) cc_final: 0.7792 (p-90)
REVERT: A  578 LYS cc_start: 0.7804 (tttm) cc_final: 0.7317 (tttp)
REVERT: A  597 ILE cc_start: 0.7729 (mp) cc_final: 0.7460 (mp)
REVERT: A  617 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5763 (mt)
REVERT: A  654 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7651 (mptt)
REVERT: A  666 LEU cc_start: 0.8703 (mm) cc_final: 0.8483 (mm)
REVERT: A  672 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7818 (mm)
REVERT: A  673 GLU cc_start: 0.7503 (tm-30) cc_final: 0.6823 (tm-30)
REVERT: A  705 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6822 (pt)
REVERT: A  710 ASN cc_start: 0.7890 (t0) cc_final: 0.7648 (t0)
REVERT: A  742 LEU cc_start: 0.8404 (tp) cc_final: 0.8173 (mp)
REVERT: A  790 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8319 (ptpp)
REVERT: A  793 LYS cc_start: 0.9010 (mttt) cc_final: 0.8484 (mttt)
REVERT: A  804 CYS cc_start: 0.2445 (OUTLIER) cc_final: 0.0906 (p)
REVERT: A  815 MET cc_start: 0.5585 (tmm) cc_final: 0.4746 (tmm)
REVERT: A  820 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7756 (tptt)
REVERT: A  834 MET cc_start: 0.7013 (tmm) cc_final: 0.6560 (tmm)
REVERT: A  888 TRP cc_start: 0.7919 (t60) cc_final: 0.6423 (t60)
REVERT: A  919 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8054 (ttpt)
REVERT: A  939 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6145 (t0)
REVERT: A  949 LEU cc_start: 0.7525 (tt) cc_final: 0.6599 (mt)
REVERT: A  956 TYR cc_start: 0.7755 (m-10) cc_final: 0.7368 (m-10)
REVERT: A 1002 MET cc_start: 0.6701 (mmm) cc_final: 0.6402 (mmm)
REVERT: A 1046 ASP cc_start: 0.7251 (p0) cc_final: 0.6972 (p0)
REVERT: A 1047 LYS cc_start: 0.7883 (tttt) cc_final: 0.7573 (tttp)
REVERT: A 1059 GLN cc_start: 0.7289 (pp30) cc_final: 0.6859 (pp30)
  outliers start: 30
  outliers final: 22
  residues processed: 180
  average time/residue: 0.2155
  time to fit residues: 49.4310
Evaluate side-chains
  194 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 552 GLN
** A 669 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 = 0.4364 r_free = 0.4364 target = 0.163038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.136801 restraints weight = 11360.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.141753 restraints weight = 6275.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.145081 restraints weight = 4032.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6580
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6367  Z= 0.203
  Angle     :  0.644   8.251   8643  Z= 0.326
  Chirality :  0.042   0.239    966
  Planarity :  0.004   0.053   1042
  Dihedral  :  9.092  84.996    898
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 30.17 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.43 (0.33), residues: 722
  helix:  0.17 (0.28), residues: 365
  sheet: -1.55 (0.77), residues: 43
  loop : -0.49 (0.40), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 888 
 HIS   0.007   0.001   HIS A 585 
 PHE   0.014   0.001   PHE A 291 
 TYR   0.022   0.001   TYR A 879 
 ARG   0.003   0.000   ARG A 680 

*********************** 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
  201 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 167
  time to evaluate  : 0.802 
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  479 GLU cc_start: 0.7105 (tp30) cc_final: 0.6679 (tp30)
REVERT: A  491 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8043 (m-80)
REVERT: A  523 ASP cc_start: 0.7781 (p0) cc_final: 0.7492 (p0)
REVERT: A  536 MET cc_start: 0.7303 (ptp) cc_final: 0.6970 (ptp)
REVERT: A  542 ILE cc_start: 0.8484 (mt) cc_final: 0.8239 (mt)
REVERT: A  560 HIS cc_start: 0.7615 (t-90) cc_final: 0.7296 (t70)
REVERT: A  578 LYS cc_start: 0.7799 (tttm) cc_final: 0.7373 (tttp)
REVERT: A  597 ILE cc_start: 0.7812 (mp) cc_final: 0.7530 (mp)
REVERT: A  607 LYS cc_start: 0.8279 (tptt) cc_final: 0.7895 (ttpt)
REVERT: A  617 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5780 (mt)
REVERT: A  618 ASN cc_start: 0.7819 (t0) cc_final: 0.7372 (m110)
REVERT: A  631 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.7052 (ttp80)
REVERT: A  651 PHE cc_start: 0.7333 (p90) cc_final: 0.6839 (p90)
REVERT: A  654 LYS cc_start: 0.7920 (mmtp) cc_final: 0.7708 (mptt)
REVERT: A  666 LEU cc_start: 0.8720 (mm) cc_final: 0.8501 (mm)
REVERT: A  672 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7864 (mm)
REVERT: A  673 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6698 (tm-30)
REVERT: A  705 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6981 (pt)
REVERT: A  710 ASN cc_start: 0.7878 (t0) cc_final: 0.7634 (t0)
REVERT: A  742 LEU cc_start: 0.8457 (tp) cc_final: 0.8209 (mp)
REVERT: A  790 LYS cc_start: 0.8591 (ptpp) cc_final: 0.8276 (ptpp)
REVERT: A  793 LYS cc_start: 0.9003 (mttt) cc_final: 0.8500 (mttt)
REVERT: A  804 CYS cc_start: 0.2364 (OUTLIER) cc_final: 0.0784 (p)
REVERT: A  815 MET cc_start: 0.5438 (tmm) cc_final: 0.4600 (tmm)
REVERT: A  820 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7725 (tptt)
REVERT: A  834 MET cc_start: 0.6827 (tmm) cc_final: 0.6404 (tmm)
REVERT: A  888 TRP cc_start: 0.7895 (t60) cc_final: 0.6490 (t60)
REVERT: A  890 TRP cc_start: 0.6888 (OUTLIER) cc_final: 0.6540 (m100)
REVERT: A  919 LYS cc_start: 0.8553 (tmtt) cc_final: 0.8112 (ttpt)
REVERT: A  939 ASN cc_start: 0.7369 (OUTLIER) cc_final: 0.6657 (t0)
REVERT: A  946 LYS cc_start: 0.8364 (tttt) cc_final: 0.8160 (tttp)
REVERT: A  949 LEU cc_start: 0.7503 (tt) cc_final: 0.6666 (mt)
REVERT: A  956 TYR cc_start: 0.7757 (m-10) cc_final: 0.7479 (m-10)
REVERT: A  965 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7776 (mmpt)
REVERT: A 1002 MET cc_start: 0.6789 (mmm) cc_final: 0.6490 (mmm)
REVERT: A 1046 ASP cc_start: 0.7338 (p0) cc_final: 0.7102 (p0)
REVERT: A 1047 LYS cc_start: 0.7868 (tttt) cc_final: 0.7578 (tttp)
  outliers start: 34
  outliers final: 24
  residues processed: 186
  average time/residue: 0.2274
  time to fit residues: 54.5598
Evaluate side-chains
  200 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
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  890 TRP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 23 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN
A 571 GLN
** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.156779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.130438 restraints weight = 11528.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.135142 restraints weight = 6528.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.138455 restraints weight = 4295.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6367  Z= 0.271
  Angle     :  0.706   8.172   8643  Z= 0.362
  Chirality :  0.045   0.245    966
  Planarity :  0.005   0.049   1042
  Dihedral  :  9.223  85.312    898
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  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: -0.58 (0.33), residues: 722
  helix:  0.03 (0.27), residues: 367
  sheet: -1.60 (0.78), residues: 43
  loop : -0.54 (0.40), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 890 
 HIS   0.008   0.001   HIS A 585 
 PHE   0.015   0.002   PHE A 759 
 TYR   0.022   0.002   TYR A 879 
 ARG   0.009   0.001   ARG A1028 

*********************** 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
  217 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 182
  time to evaluate  : 0.699 
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  463 ASN cc_start: 0.8024 (m-40) cc_final: 0.7787 (m-40)
REVERT: A  479 GLU cc_start: 0.7188 (tp30) cc_final: 0.6870 (tp30)
REVERT: A  536 MET cc_start: 0.7272 (ptp) cc_final: 0.6954 (ptp)
REVERT: A  560 HIS cc_start: 0.7627 (t-90) cc_final: 0.7256 (t-90)
REVERT: A  562 ASP cc_start: 0.7917 (m-30) cc_final: 0.7682 (p0)
REVERT: A  597 ILE cc_start: 0.7864 (mp) cc_final: 0.7585 (mp)
REVERT: A  607 LYS cc_start: 0.8273 (tptt) cc_final: 0.7981 (ttpt)
REVERT: A  617 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5979 (tp)
REVERT: A  636 LYS cc_start: 0.8407 (pttp) cc_final: 0.7470 (mtmm)
REVERT: A  651 PHE cc_start: 0.7247 (p90) cc_final: 0.6766 (p90)
REVERT: A  654 LYS cc_start: 0.7968 (mmtp) cc_final: 0.7748 (mptt)
REVERT: A  666 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8471 (mm)
REVERT: A  672 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7875 (mm)
REVERT: A  673 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6871 (tm-30)
REVERT: A  705 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7083 (pt)
REVERT: A  710 ASN cc_start: 0.7886 (t0) cc_final: 0.7591 (t0)
REVERT: A  742 LEU cc_start: 0.8434 (tp) cc_final: 0.8158 (mp)
REVERT: A  768 TYR cc_start: 0.6041 (t80) cc_final: 0.5754 (t80)
REVERT: A  772 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6470 (mm110)
REVERT: A  790 LYS cc_start: 0.8619 (ptpp) cc_final: 0.8308 (ptpp)
REVERT: A  793 LYS cc_start: 0.9028 (mttt) cc_final: 0.8524 (mttt)
REVERT: A  804 CYS cc_start: 0.2388 (OUTLIER) cc_final: 0.0815 (p)
REVERT: A  815 MET cc_start: 0.5524 (tmm) cc_final: 0.4707 (tmm)
REVERT: A  820 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7785 (tptt)
REVERT: A  834 MET cc_start: 0.6841 (tmm) cc_final: 0.6406 (tmm)
REVERT: A  888 TRP cc_start: 0.7961 (t60) cc_final: 0.6508 (t60)
REVERT: A  890 TRP cc_start: 0.7002 (OUTLIER) cc_final: 0.6654 (m100)
REVERT: A  919 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8146 (ttpt)
REVERT: A  939 ASN cc_start: 0.7460 (OUTLIER) cc_final: 0.6525 (t0)
REVERT: A  949 LEU cc_start: 0.7660 (tt) cc_final: 0.6748 (mt)
REVERT: A  956 TYR cc_start: 0.7798 (m-10) cc_final: 0.7570 (m-10)
REVERT: A  965 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7752 (mmpt)
REVERT: A 1002 MET cc_start: 0.6797 (mmm) cc_final: 0.6503 (mmm)
REVERT: A 1031 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.7005 (ptt180)
REVERT: A 1038 LYS cc_start: 0.7665 (tppp) cc_final: 0.7120 (tptp)
REVERT: A 1046 ASP cc_start: 0.7506 (p0) cc_final: 0.7253 (p0)
REVERT: A 1047 LYS cc_start: 0.7906 (tttt) cc_final: 0.7614 (tttp)
  outliers start: 35
  outliers final: 22
  residues processed: 200
  average time/residue: 0.2129
  time to fit residues: 54.3879
Evaluate side-chains
  212 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
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  890 TRP
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  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1031 ARG
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:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   chunk 44 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0470
   chunk 61 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0040
   overall best weight:    0.3490

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4337 r_free = 0.4337 target = 0.160799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.133726 restraints weight = 11578.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.138750 restraints weight = 6594.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.142251 restraints weight = 4324.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6367  Z= 0.197
  Angle     :  0.705   8.853   8643  Z= 0.359
  Chirality :  0.043   0.219    966
  Planarity :  0.005   0.053   1042
  Dihedral  :  9.042  85.494    898
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 31.98 %
    Favored  : 64.25 %
  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: -0.47 (0.33), residues: 722
  helix:  0.07 (0.28), residues: 366
  sheet: -1.54 (0.79), residues: 43
  loop : -0.42 (0.41), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 890 
 HIS   0.012   0.002   HIS A 554 
 PHE   0.012   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 414 
 ARG   0.009   0.001   ARG A1028 

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

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.645 
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  292 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8656 (mmtt)
REVERT: A  479 GLU cc_start: 0.7123 (tp30) cc_final: 0.6771 (tp30)
REVERT: A  491 PHE cc_start: 0.8380 (m-10) cc_final: 0.8151 (m-80)
REVERT: A  536 MET cc_start: 0.7208 (ptp) cc_final: 0.6856 (ptp)
REVERT: A  560 HIS cc_start: 0.7655 (t-90) cc_final: 0.7279 (t70)
REVERT: A  578 LYS cc_start: 0.7723 (tttm) cc_final: 0.7423 (tttp)
REVERT: A  597 ILE cc_start: 0.7827 (mp) cc_final: 0.7545 (mp)
REVERT: A  607 LYS cc_start: 0.8200 (tptt) cc_final: 0.7895 (ttpt)
REVERT: A  617 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5838 (tp)
REVERT: A  636 LYS cc_start: 0.8377 (pttp) cc_final: 0.7186 (tmmt)
REVERT: A  651 PHE cc_start: 0.7240 (p90) cc_final: 0.6749 (p90)
REVERT: A  654 LYS cc_start: 0.7947 (mmtp) cc_final: 0.7727 (mptt)
REVERT: A  672 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7592 (mm)
REVERT: A  673 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6823 (tm-30)
REVERT: A  705 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7045 (pt)
REVERT: A  710 ASN cc_start: 0.7873 (t0) cc_final: 0.7570 (t0)
REVERT: A  742 LEU cc_start: 0.8459 (tp) cc_final: 0.8205 (mp)
REVERT: A  768 TYR cc_start: 0.5871 (t80) cc_final: 0.5620 (t80)
REVERT: A  772 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6383 (mm110)
REVERT: A  790 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8336 (ptpp)
REVERT: A  793 LYS cc_start: 0.8993 (mttt) cc_final: 0.8476 (mttt)
REVERT: A  804 CYS cc_start: 0.2373 (OUTLIER) cc_final: 0.0835 (p)
REVERT: A  815 MET cc_start: 0.5483 (tmm) cc_final: 0.4679 (tmm)
REVERT: A  820 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7784 (tptt)
REVERT: A  834 MET cc_start: 0.6785 (tmm) cc_final: 0.6307 (tmm)
REVERT: A  888 TRP cc_start: 0.7915 (t60) cc_final: 0.6724 (t60)
REVERT: A  890 TRP cc_start: 0.6860 (OUTLIER) cc_final: 0.6504 (m100)
REVERT: A  919 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8137 (ttpt)
REVERT: A  956 TYR cc_start: 0.7760 (m-10) cc_final: 0.7216 (m-10)
REVERT: A  965 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7723 (mmpt)
REVERT: A  978 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7717 (mt-10)
REVERT: A 1002 MET cc_start: 0.6770 (mmm) cc_final: 0.6477 (mmm)
REVERT: A 1038 LYS cc_start: 0.7618 (tppp) cc_final: 0.7083 (tppt)
REVERT: A 1040 PHE cc_start: 0.7650 (m-80) cc_final: 0.7405 (m-80)
REVERT: A 1046 ASP cc_start: 0.7484 (p0) cc_final: 0.7261 (p0)
REVERT: A 1047 LYS cc_start: 0.7866 (tttt) cc_final: 0.7587 (tttp)
REVERT: A 1058 LYS cc_start: 0.8142 (tppt) cc_final: 0.7681 (mttt)
  outliers start: 25
  outliers final: 17
  residues processed: 189
  average time/residue: 0.2239
  time to fit residues: 53.7714
Evaluate side-chains
  194 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  794 GLU
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  890 TRP
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1035 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0770
   chunk 51 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0060
   chunk 68 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 46 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0170
   overall best weight:    0.1992

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4393 r_free = 0.4393 target = 0.165383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.137342 restraints weight = 11650.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.142212 restraints weight = 6746.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.145808 restraints weight = 4523.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6551
moved from start:          0.4499

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= 0.189
  Angle     :  0.698   8.477   8643  Z= 0.355
  Chirality :  0.043   0.216    966
  Planarity :  0.005   0.057   1042
  Dihedral  :  8.880  84.609    898
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 31.37 %
    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: -0.38 (0.33), residues: 722
  helix:  0.24 (0.28), residues: 353
  sheet: -1.52 (0.79), residues: 43
  loop : -0.48 (0.40), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 890 
 HIS   0.003   0.001   HIS A 554 
 PHE   0.014   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 707 
 ARG   0.008   0.001   ARG A1028 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3559.16 seconds
wall clock time: 61 minutes 59.97 seconds (3719.97 seconds total)