Starting phenix.real_space_refine
on Thu Nov 14 12:33:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/11_2024/8sxu_40859.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/11_2024/8sxu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/11_2024/8sxu_40859.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/11_2024/8sxu_40859.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/11_2024/8sxu_40859.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/11_2024/8sxu_40859.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      20      5.16       5
     C    3981      2.51       5
     N    1064      2.21       5
     O    1132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.14, per 1000 atoms: 0.67
  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: 1.64
  Conformation dependent library (CDL) restraints added in 793.9 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: 2.01
  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: 1.96

  Time building geometry restraints manager: 1.81 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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.450
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:   23.560
-------------------------------------------------------------------------------
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  : 0.699 
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  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: 0.2320
  time to fit residues: 51.0518
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  : 0.726 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
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  : 0.736 
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: 0.3079 (mmt) cc_final: 0.2837 (mmt)
REVERT: A  505 LEU cc_start: 0.7753 (mp) cc_final: 0.7524 (mp)
REVERT: A  536 MET cc_start: 0.6882 (ptp) cc_final: 0.6475 (ptp)
REVERT: A  538 ILE cc_start: 0.7733 (mm) cc_final: 0.7404 (mp)
REVERT: A  539 ASP cc_start: 0.7815 (p0) cc_final: 0.7444 (p0)
REVERT: A  542 ILE cc_start: 0.8469 (mt) cc_final: 0.8263 (mt)
REVERT: A  545 LYS cc_start: 0.8470 (tttt) cc_final: 0.8187 (mttt)
REVERT: A  560 HIS cc_start: 0.7243 (t-90) cc_final: 0.6784 (t-90)
REVERT: A  596 ILE cc_start: 0.7170 (mm) cc_final: 0.6922 (tt)
REVERT: A  627 LEU cc_start: 0.7287 (mt) cc_final: 0.6915 (mt)
REVERT: A  651 PHE cc_start: 0.7408 (p90) cc_final: 0.6680 (p90)
REVERT: A  654 LYS cc_start: 0.7421 (mmtp) cc_final: 0.7184 (mptt)
REVERT: A  663 LEU cc_start: 0.8209 (tp) cc_final: 0.7957 (pt)
REVERT: A  666 LEU cc_start: 0.8715 (mm) cc_final: 0.8454 (mm)
REVERT: A  673 GLU cc_start: 0.7652 (tm-30) cc_final: 0.6859 (tm-30)
REVERT: A  681 GLN cc_start: 0.8176 (mm110) cc_final: 0.7918 (mm-40)
REVERT: A  710 ASN cc_start: 0.7624 (t0) cc_final: 0.7309 (p0)
REVERT: A  720 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8493 (mtmm)
REVERT: A  759 PHE cc_start: 0.7551 (m-80) cc_final: 0.7022 (m-80)
REVERT: A  766 ILE cc_start: 0.7369 (pt) cc_final: 0.6999 (pt)
REVERT: A  772 GLN cc_start: 0.6527 (mm-40) cc_final: 0.6245 (mm-40)
REVERT: A  789 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7302 (pp)
REVERT: A  790 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8121 (ptpp)
REVERT: A  793 LYS cc_start: 0.8916 (mttt) cc_final: 0.8344 (mttt)
REVERT: A  815 MET cc_start: 0.5965 (tmm) cc_final: 0.5214 (tmm)
REVERT: A  823 TYR cc_start: 0.8132 (t80) cc_final: 0.7815 (t80)
REVERT: A  834 MET cc_start: 0.7239 (tmm) cc_final: 0.6965 (tmm)
REVERT: A  837 PHE cc_start: 0.8094 (m-80) cc_final: 0.7853 (m-80)
REVERT: A  876 LYS cc_start: 0.7712 (tptt) cc_final: 0.7419 (tptt)
REVERT: A  919 LYS cc_start: 0.7974 (tmtt) cc_final: 0.7606 (ttpt)
REVERT: A  997 LYS cc_start: 0.7524 (ttmm) cc_final: 0.7309 (mtmt)
REVERT: A 1058 LYS cc_start: 0.8312 (ttmm) cc_final: 0.8004 (ttmm)
  outliers start: 33
  outliers final: 20
  residues processed: 189
  average time/residue: 0.2144
  time to fit residues: 51.6855
Evaluate side-chains
  175 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  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 1031 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0770
   chunk 55 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0060
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0470
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.2852

-------------------------------------------------------------------------------
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 571 GLN
A 669 ASN
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1055 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6367  Z= 0.174
  Angle     :  0.615   7.668   8643  Z= 0.315
  Chirality :  0.041   0.160    966
  Planarity :  0.004   0.052   1042
  Dihedral  :  9.880 116.965    898
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 27.45 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.32), residues: 722
  helix:  0.20 (0.28), residues: 352
  sheet: -1.09 (0.82), residues: 43
  loop : -0.62 (0.38), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 288 
 HIS   0.001   0.000   HIS A 910 
 PHE   0.013   0.001   PHE A 781 
 TYR   0.009   0.001   TYR A1054 
 ARG   0.006   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
  198 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    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: symmetry clash
REVERT: A  266 MET cc_start: 0.3112 (mmt) cc_final: 0.2866 (mmt)
REVERT: A  288 TRP cc_start: 0.8120 (t-100) cc_final: 0.7744 (t-100)
REVERT: A  292 LYS cc_start: 0.8687 (mttp) cc_final: 0.8403 (mttp)
REVERT: A  491 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8624 (m-80)
REVERT: A  495 LEU cc_start: 0.7050 (tt) cc_final: 0.6833 (tp)
REVERT: A  505 LEU cc_start: 0.7745 (mp) cc_final: 0.7486 (mp)
REVERT: A  510 TYR cc_start: 0.6535 (m-80) cc_final: 0.6315 (m-80)
REVERT: A  531 ARG cc_start: 0.2442 (mmt180) cc_final: 0.1919 (tpt170)
REVERT: A  536 MET cc_start: 0.6904 (ptp) cc_final: 0.6469 (ptp)
REVERT: A  538 ILE cc_start: 0.7732 (mm) cc_final: 0.7391 (mp)
REVERT: A  539 ASP cc_start: 0.7813 (p0) cc_final: 0.7558 (p0)
REVERT: A  542 ILE cc_start: 0.8464 (mt) cc_final: 0.8251 (mt)
REVERT: A  545 LYS cc_start: 0.8449 (tttt) cc_final: 0.8185 (mttt)
REVERT: A  560 HIS cc_start: 0.7247 (t-90) cc_final: 0.6819 (t-90)
REVERT: A  578 LYS cc_start: 0.7762 (tttm) cc_final: 0.7279 (tttp)
REVERT: A  597 ILE cc_start: 0.7519 (mp) cc_final: 0.7119 (mm)
REVERT: A  607 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6627 (tmmt)
REVERT: A  618 ASN cc_start: 0.7547 (t0) cc_final: 0.7201 (m-40)
REVERT: A  640 ASN cc_start: 0.7077 (p0) cc_final: 0.6853 (p0)
REVERT: A  651 PHE cc_start: 0.7458 (p90) cc_final: 0.6721 (p90)
REVERT: A  654 LYS cc_start: 0.7445 (mmtp) cc_final: 0.7135 (mptt)
REVERT: A  673 GLU cc_start: 0.7689 (tm-30) cc_final: 0.6881 (tm-30)
REVERT: A  710 ASN cc_start: 0.7617 (t0) cc_final: 0.7355 (p0)
REVERT: A  766 ILE cc_start: 0.7342 (pt) cc_final: 0.6985 (pt)
REVERT: A  772 GLN cc_start: 0.6574 (mm-40) cc_final: 0.6315 (mm-40)
REVERT: A  789 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7355 (pp)
REVERT: A  790 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8122 (ptpp)
REVERT: A  793 LYS cc_start: 0.8911 (mttt) cc_final: 0.8352 (mttt)
REVERT: A  815 MET cc_start: 0.5949 (tmm) cc_final: 0.5193 (tmm)
REVERT: A  820 LYS cc_start: 0.8280 (tptt) cc_final: 0.8075 (tptt)
REVERT: A  823 TYR cc_start: 0.8104 (t80) cc_final: 0.7719 (t80)
REVERT: A  834 MET cc_start: 0.7195 (tmm) cc_final: 0.6831 (tmm)
REVERT: A  876 LYS cc_start: 0.7761 (tptt) cc_final: 0.7524 (tptt)
REVERT: A  939 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6047 (t0)
REVERT: A  949 LEU cc_start: 0.7324 (tt) cc_final: 0.6210 (mt)
REVERT: A  997 LYS cc_start: 0.7504 (ttmm) cc_final: 0.7294 (mtmt)
  outliers start: 32
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2218
  time to fit residues: 51.9619
Evaluate side-chains
  185 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  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  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  675 LEU
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1031 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    0.4980
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6678
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6367  Z= 0.191
  Angle     :  0.619  11.064   8643  Z= 0.313
  Chirality :  0.042   0.151    966
  Planarity :  0.004   0.053   1042
  Dihedral  :  9.733 110.682    898
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 12.95
  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: -0.46 (0.32), residues: 722
  helix:  0.21 (0.28), residues: 352
  sheet: -1.19 (0.80), residues: 43
  loop : -0.62 (0.37), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 573 
 HIS   0.002   0.001   HIS A 910 
 PHE   0.016   0.001   PHE A 781 
 TYR   0.014   0.001   TYR A 414 
 ARG   0.005   0.001   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
  213 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.708 
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  266 MET cc_start: 0.3177 (mmt) cc_final: 0.2945 (mmt)
REVERT: A  288 TRP cc_start: 0.8194 (t-100) cc_final: 0.7751 (t-100)
REVERT: A  292 LYS cc_start: 0.8771 (mttp) cc_final: 0.8463 (mttp)
REVERT: A  413 GLU cc_start: 0.7206 (tp30) cc_final: 0.7005 (tp30)
REVERT: A  428 GLU cc_start: 0.7351 (mp0) cc_final: 0.6919 (mp0)
REVERT: A  491 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8625 (m-80)
REVERT: A  505 LEU cc_start: 0.7783 (mp) cc_final: 0.7482 (mp)
REVERT: A  531 ARG cc_start: 0.2128 (mmt180) cc_final: 0.1830 (tpt170)
REVERT: A  536 MET cc_start: 0.6990 (ptp) cc_final: 0.6475 (ptp)
REVERT: A  538 ILE cc_start: 0.7685 (mm) cc_final: 0.7360 (mp)
REVERT: A  539 ASP cc_start: 0.7834 (p0) cc_final: 0.7435 (p0)
REVERT: A  542 ILE cc_start: 0.8459 (mt) cc_final: 0.8242 (mt)
REVERT: A  545 LYS cc_start: 0.8456 (tttt) cc_final: 0.8185 (mttt)
REVERT: A  560 HIS cc_start: 0.7355 (t-90) cc_final: 0.6783 (t-90)
REVERT: A  597 ILE cc_start: 0.7525 (mp) cc_final: 0.7132 (mm)
REVERT: A  607 LYS cc_start: 0.6981 (ttpt) cc_final: 0.6562 (tmmt)
REVERT: A  618 ASN cc_start: 0.7607 (t0) cc_final: 0.7206 (m-40)
REVERT: A  631 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6848 (ttp80)
REVERT: A  651 PHE cc_start: 0.7453 (p90) cc_final: 0.6799 (p90)
REVERT: A  654 LYS cc_start: 0.7508 (mmtp) cc_final: 0.7269 (mptt)
REVERT: A  673 GLU cc_start: 0.7704 (tm-30) cc_final: 0.6930 (tm-30)
REVERT: A  742 LEU cc_start: 0.8432 (tp) cc_final: 0.8170 (mp)
REVERT: A  746 ASN cc_start: 0.7418 (t0) cc_final: 0.7006 (p0)
REVERT: A  766 ILE cc_start: 0.7342 (pt) cc_final: 0.6889 (pt)
REVERT: A  772 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6333 (mm110)
REVERT: A  789 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7401 (pp)
REVERT: A  790 LYS cc_start: 0.8740 (ptpp) cc_final: 0.8184 (ptpp)
REVERT: A  793 LYS cc_start: 0.8930 (mttt) cc_final: 0.8374 (mttt)
REVERT: A  815 MET cc_start: 0.5979 (tmm) cc_final: 0.5216 (tmm)
REVERT: A  820 LYS cc_start: 0.8359 (tptt) cc_final: 0.7640 (tptt)
REVERT: A  823 TYR cc_start: 0.8161 (t80) cc_final: 0.7746 (t80)
REVERT: A  834 MET cc_start: 0.7129 (tmm) cc_final: 0.6752 (tmm)
REVERT: A  876 LYS cc_start: 0.7805 (tptt) cc_final: 0.7561 (tptt)
REVERT: A  898 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6720 (tm-30)
REVERT: A  939 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6396 (m-40)
REVERT: A  949 LEU cc_start: 0.7379 (tt) cc_final: 0.6260 (mt)
REVERT: A 1028 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7658 (tpp80)
REVERT: A 1059 GLN cc_start: 0.7445 (pp30) cc_final: 0.7054 (pp30)
  outliers start: 37
  outliers final: 22
  residues processed: 197
  average time/residue: 0.2248
  time to fit residues: 55.9956
Evaluate side-chains
  193 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  756 GLU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  990 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 659 GLN
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6367  Z= 0.186
  Angle     :  0.603   9.016   8643  Z= 0.306
  Chirality :  0.042   0.150    966
  Planarity :  0.004   0.052   1042
  Dihedral  :  9.456  99.688    898
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 27.60 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.33), residues: 722
  helix:  0.28 (0.28), residues: 356
  sheet: -1.15 (0.80), residues: 43
  loop : -0.61 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 288 
 HIS   0.009   0.001   HIS A 585 
 PHE   0.019   0.001   PHE A 836 
 TYR   0.011   0.001   TYR A 414 
 ARG   0.004   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
  206 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 167
  time to evaluate  : 0.729 
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: 0.3181 (mmt) cc_final: 0.2950 (mmt)
REVERT: A  292 LYS cc_start: 0.8869 (mttp) cc_final: 0.8559 (mttp)
REVERT: A  413 GLU cc_start: 0.7224 (tp30) cc_final: 0.7003 (tp30)
REVERT: A  428 GLU cc_start: 0.7337 (mp0) cc_final: 0.6949 (mp0)
REVERT: A  491 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8582 (m-80)
REVERT: A  505 LEU cc_start: 0.7686 (mp) cc_final: 0.7387 (mp)
REVERT: A  531 ARG cc_start: 0.1920 (mmt180) cc_final: 0.1641 (tpt170)
REVERT: A  536 MET cc_start: 0.7000 (ptp) cc_final: 0.6444 (ptp)
REVERT: A  538 ILE cc_start: 0.7639 (mm) cc_final: 0.7296 (mp)
REVERT: A  539 ASP cc_start: 0.7864 (p0) cc_final: 0.7556 (p0)
REVERT: A  542 ILE cc_start: 0.8464 (mt) cc_final: 0.8222 (mt)
REVERT: A  560 HIS cc_start: 0.7475 (t-90) cc_final: 0.6797 (t-90)
REVERT: A  578 LYS cc_start: 0.7776 (tttm) cc_final: 0.7296 (tttp)
REVERT: A  597 ILE cc_start: 0.7494 (mp) cc_final: 0.7080 (mm)
REVERT: A  631 ARG cc_start: 0.7056 (ttm-80) cc_final: 0.6783 (ttp80)
REVERT: A  651 PHE cc_start: 0.7420 (p90) cc_final: 0.6885 (p90)
REVERT: A  654 LYS cc_start: 0.7528 (mmtp) cc_final: 0.7276 (mptt)
REVERT: A  672 LEU cc_start: 0.8391 (mm) cc_final: 0.7987 (mm)
REVERT: A  673 GLU cc_start: 0.7735 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: A  681 GLN cc_start: 0.8260 (mm110) cc_final: 0.8025 (mm-40)
REVERT: A  742 LEU cc_start: 0.8459 (tp) cc_final: 0.8196 (mp)
REVERT: A  746 ASN cc_start: 0.7410 (t0) cc_final: 0.6999 (p0)
REVERT: A  789 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7468 (pp)
REVERT: A  790 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8369 (ptpp)
REVERT: A  793 LYS cc_start: 0.8938 (mttt) cc_final: 0.8388 (mttt)
REVERT: A  804 CYS cc_start: 0.2837 (OUTLIER) cc_final: 0.0978 (p)
REVERT: A  809 ARG cc_start: 0.8170 (mmp80) cc_final: 0.7925 (mpp-170)
REVERT: A  815 MET cc_start: 0.5980 (tmm) cc_final: 0.5190 (tmm)
REVERT: A  820 LYS cc_start: 0.8425 (tptt) cc_final: 0.7721 (tptt)
REVERT: A  823 TYR cc_start: 0.8113 (t80) cc_final: 0.7721 (t80)
REVERT: A  834 MET cc_start: 0.7148 (tmm) cc_final: 0.6622 (tmm)
REVERT: A  837 PHE cc_start: 0.8096 (m-80) cc_final: 0.7115 (m-80)
REVERT: A  876 LYS cc_start: 0.7831 (tptt) cc_final: 0.7628 (tptt)
REVERT: A  932 LEU cc_start: 0.1817 (OUTLIER) cc_final: 0.0345 (mt)
REVERT: A  939 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6038 (t0)
REVERT: A  949 LEU cc_start: 0.7410 (tt) cc_final: 0.6377 (mt)
REVERT: A 1028 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7676 (tpp80)
  outliers start: 39
  outliers final: 25
  residues processed: 188
  average time/residue: 0.2164
  time to fit residues: 51.7036
Evaluate side-chains
  192 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  675 LEU
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  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  804 CYS
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  977 LEU
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1031 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0030
   chunk 17 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0020
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0770
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.2756

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

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
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   0.040   6367  Z= 0.175
  Angle     :  0.624   9.432   8643  Z= 0.308
  Chirality :  0.041   0.263    966
  Planarity :  0.004   0.054   1042
  Dihedral  :  9.219  92.737    898
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 29.26 %
    Favored  : 66.06 %
  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: -0.23 (0.33), residues: 722
  helix:  0.41 (0.29), residues: 349
  sheet: -1.15 (0.79), residues: 43
  loop : -0.50 (0.38), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 288 
 HIS   0.006   0.001   HIS A 585 
 PHE   0.007   0.001   PHE A 612 
 TYR   0.011   0.001   TYR A 634 
 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
  202 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 0.644 
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: 0.3158 (mmt) cc_final: 0.2935 (mmt)
REVERT: A  285 GLN cc_start: 0.7233 (mp10) cc_final: 0.6978 (mp10)
REVERT: A  413 GLU cc_start: 0.7219 (tp30) cc_final: 0.7007 (tp30)
REVERT: A  414 TYR cc_start: 0.8082 (t80) cc_final: 0.7674 (t80)
REVERT: A  428 GLU cc_start: 0.7307 (mp0) cc_final: 0.6849 (mp0)
REVERT: A  443 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: A  479 GLU cc_start: 0.6617 (tp30) cc_final: 0.6186 (tp30)
REVERT: A  491 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8490 (m-80)
REVERT: A  505 LEU cc_start: 0.7646 (mp) cc_final: 0.7389 (mp)
REVERT: A  536 MET cc_start: 0.6947 (ptp) cc_final: 0.6433 (ptp)
REVERT: A  538 ILE cc_start: 0.7636 (mm) cc_final: 0.7287 (mp)
REVERT: A  539 ASP cc_start: 0.7894 (p0) cc_final: 0.7596 (p0)
REVERT: A  542 ILE cc_start: 0.8431 (mt) cc_final: 0.8231 (mt)
REVERT: A  560 HIS cc_start: 0.7464 (t-90) cc_final: 0.6856 (t-90)
REVERT: A  597 ILE cc_start: 0.7395 (mp) cc_final: 0.7008 (mm)
REVERT: A  607 LYS cc_start: 0.7692 (tppt) cc_final: 0.7155 (tmmt)
REVERT: A  651 PHE cc_start: 0.7442 (p90) cc_final: 0.6869 (p90)
REVERT: A  654 LYS cc_start: 0.7470 (mmtp) cc_final: 0.7227 (mptt)
REVERT: A  672 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7943 (mm)
REVERT: A  673 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: A  742 LEU cc_start: 0.8449 (tp) cc_final: 0.8163 (mp)
REVERT: A  746 ASN cc_start: 0.7475 (t0) cc_final: 0.7221 (p0)
REVERT: A  766 ILE cc_start: 0.7225 (pt) cc_final: 0.6291 (mt)
REVERT: A  772 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6332 (mm110)
REVERT: A  790 LYS cc_start: 0.8794 (ptpp) cc_final: 0.8399 (ptpp)
REVERT: A  793 LYS cc_start: 0.8934 (mttt) cc_final: 0.8364 (mttt)
REVERT: A  804 CYS cc_start: 0.2832 (OUTLIER) cc_final: 0.1599 (p)
REVERT: A  815 MET cc_start: 0.5958 (tmm) cc_final: 0.5174 (tmm)
REVERT: A  820 LYS cc_start: 0.8401 (tptt) cc_final: 0.7722 (tptt)
REVERT: A  834 MET cc_start: 0.7099 (tmm) cc_final: 0.6548 (tmm)
REVERT: A  837 PHE cc_start: 0.8020 (m-80) cc_final: 0.7181 (m-80)
REVERT: A  876 LYS cc_start: 0.7816 (tptt) cc_final: 0.7612 (tptt)
REVERT: A  879 TYR cc_start: 0.8179 (t80) cc_final: 0.7930 (t80)
REVERT: A  932 LEU cc_start: 0.1859 (OUTLIER) cc_final: 0.0448 (mt)
REVERT: A  939 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.5997 (t0)
REVERT: A  949 LEU cc_start: 0.7395 (tt) cc_final: 0.6409 (mt)
REVERT: A  978 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: A 1058 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7958 (ttmm)
REVERT: A 1059 GLN cc_start: 0.7213 (pp30) cc_final: 0.6915 (pp30)
  outliers start: 31
  outliers final: 19
  residues processed: 185
  average time/residue: 0.2306
  time to fit residues: 54.3373
Evaluate side-chains
  188 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  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  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 7 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0050
   chunk 39 optimal weight:    0.6980
   chunk 59 optimal weight:    0.3980
   chunk 70 optimal weight:    0.0770
   chunk 44 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0070
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.2170

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.3516

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= 0.177
  Angle     :  0.620   8.039   8643  Z= 0.307
  Chirality :  0.041   0.214    966
  Planarity :  0.004   0.056   1042
  Dihedral  :  9.038  87.088    898
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 28.96 %
    Favored  : 66.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.33), residues: 722
  helix:  0.42 (0.29), residues: 349
  sheet: -1.24 (0.78), residues: 43
  loop : -0.45 (0.38), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 573 
 HIS   0.004   0.001   HIS A 585 
 PHE   0.007   0.001   PHE A 612 
 TYR   0.011   0.001   TYR A 634 
 ARG   0.003   0.000   ARG A 680 

*********************** 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
  199 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7311 (mp10) cc_final: 0.6946 (mp10)
REVERT: A  413 GLU cc_start: 0.7191 (tp30) cc_final: 0.6978 (tp30)
REVERT: A  414 TYR cc_start: 0.8057 (t80) cc_final: 0.7621 (t80)
REVERT: A  443 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8160 (tm-30)
REVERT: A  479 GLU cc_start: 0.6666 (tp30) cc_final: 0.6180 (tp30)
REVERT: A  491 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8447 (m-80)
REVERT: A  505 LEU cc_start: 0.7749 (mp) cc_final: 0.7422 (mp)
REVERT: A  536 MET cc_start: 0.6951 (ptp) cc_final: 0.6480 (ptp)
REVERT: A  538 ILE cc_start: 0.7651 (mm) cc_final: 0.7288 (mp)
REVERT: A  539 ASP cc_start: 0.7952 (p0) cc_final: 0.7559 (p0)
REVERT: A  560 HIS cc_start: 0.7443 (t-90) cc_final: 0.6851 (t-90)
REVERT: A  597 ILE cc_start: 0.7384 (mp) cc_final: 0.6992 (mm)
REVERT: A  607 LYS cc_start: 0.7796 (tppt) cc_final: 0.7279 (tmmt)
REVERT: A  618 ASN cc_start: 0.7575 (t0) cc_final: 0.7246 (m-40)
REVERT: A  651 PHE cc_start: 0.7434 (p90) cc_final: 0.6853 (p90)
REVERT: A  654 LYS cc_start: 0.7473 (mmtp) cc_final: 0.7236 (mptt)
REVERT: A  672 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7818 (mm)
REVERT: A  673 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7081 (tm-30)
REVERT: A  742 LEU cc_start: 0.8468 (tp) cc_final: 0.8190 (mp)
REVERT: A  766 ILE cc_start: 0.7192 (pt) cc_final: 0.6282 (mt)
REVERT: A  772 GLN cc_start: 0.6855 (mm-40) cc_final: 0.6318 (mm110)
REVERT: A  790 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8427 (ptpp)
REVERT: A  793 LYS cc_start: 0.8946 (mttt) cc_final: 0.8405 (mttt)
REVERT: A  804 CYS cc_start: 0.2806 (OUTLIER) cc_final: 0.0897 (p)
REVERT: A  809 ARG cc_start: 0.8172 (mmp80) cc_final: 0.7902 (mpp-170)
REVERT: A  815 MET cc_start: 0.5983 (tmm) cc_final: 0.5193 (tmm)
REVERT: A  820 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7749 (tptt)
REVERT: A  834 MET cc_start: 0.7081 (tmm) cc_final: 0.6504 (tmm)
REVERT: A  837 PHE cc_start: 0.8052 (m-80) cc_final: 0.7132 (m-80)
REVERT: A  876 LYS cc_start: 0.7811 (tptt) cc_final: 0.7602 (tptt)
REVERT: A  879 TYR cc_start: 0.8188 (t80) cc_final: 0.7955 (t80)
REVERT: A  939 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.5944 (t0)
REVERT: A  949 LEU cc_start: 0.7368 (tt) cc_final: 0.6410 (mt)
REVERT: A 1028 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7634 (tpp80)
  outliers start: 32
  outliers final: 22
  residues processed: 185
  average time/residue: 0.1769
  time to fit residues: 42.1430
Evaluate side-chains
  190 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  675 LEU
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  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  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 42 optimal weight:    0.0970
   chunk 21 optimal weight:    0.0770
   chunk 13 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 64 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.2934

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.3658

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= 0.178
  Angle     :  0.629  10.117   8643  Z= 0.311
  Chirality :  0.041   0.200    966
  Planarity :  0.004   0.056   1042
  Dihedral  :  8.934  83.689    898
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 30.47 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.33), residues: 722
  helix:  0.29 (0.28), residues: 355
  sheet: -1.22 (0.79), residues: 43
  loop : -0.41 (0.39), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 573 
 HIS   0.003   0.001   HIS A 585 
 PHE   0.014   0.001   PHE A 291 
 TYR   0.010   0.001   TYR A1054 
 ARG   0.006   0.000   ARG A 631 

*********************** 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
  195 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7310 (mp10) cc_final: 0.6936 (mp10)
REVERT: A  406 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7488 (pp20)
REVERT: A  413 GLU cc_start: 0.7217 (tp30) cc_final: 0.6999 (tp30)
REVERT: A  414 TYR cc_start: 0.8058 (t80) cc_final: 0.7611 (t80)
REVERT: A  443 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8310 (tm-30)
REVERT: A  447 GLU cc_start: 0.8797 (tt0) cc_final: 0.8030 (tm-30)
REVERT: A  479 GLU cc_start: 0.6681 (tp30) cc_final: 0.6167 (tp30)
REVERT: A  491 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8436 (m-80)
REVERT: A  505 LEU cc_start: 0.7743 (mp) cc_final: 0.7425 (mp)
REVERT: A  536 MET cc_start: 0.6968 (ptp) cc_final: 0.6501 (ptp)
REVERT: A  539 ASP cc_start: 0.7871 (p0) cc_final: 0.7659 (p0)
REVERT: A  560 HIS cc_start: 0.7427 (t-90) cc_final: 0.6799 (t-90)
REVERT: A  578 LYS cc_start: 0.7755 (tttm) cc_final: 0.7415 (tttp)
REVERT: A  597 ILE cc_start: 0.7431 (mp) cc_final: 0.7042 (mm)
REVERT: A  607 LYS cc_start: 0.7834 (tppt) cc_final: 0.7272 (tmmt)
REVERT: A  651 PHE cc_start: 0.7430 (p90) cc_final: 0.6842 (p90)
REVERT: A  654 LYS cc_start: 0.7471 (mmtp) cc_final: 0.7229 (mptt)
REVERT: A  672 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7921 (mm)
REVERT: A  673 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7103 (tm-30)
REVERT: A  742 LEU cc_start: 0.8451 (tp) cc_final: 0.8231 (mp)
REVERT: A  772 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6362 (mm110)
REVERT: A  790 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8395 (ptpp)
REVERT: A  793 LYS cc_start: 0.8951 (mttt) cc_final: 0.8416 (mttt)
REVERT: A  804 CYS cc_start: 0.2706 (OUTLIER) cc_final: 0.1462 (p)
REVERT: A  815 MET cc_start: 0.5957 (tmm) cc_final: 0.5167 (tmm)
REVERT: A  820 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7691 (tptt)
REVERT: A  834 MET cc_start: 0.7033 (tmm) cc_final: 0.6428 (tmm)
REVERT: A  837 PHE cc_start: 0.8084 (m-80) cc_final: 0.7109 (m-80)
REVERT: A  876 LYS cc_start: 0.7832 (tptt) cc_final: 0.7611 (tptt)
REVERT: A  879 TYR cc_start: 0.8217 (t80) cc_final: 0.7972 (t80)
REVERT: A  939 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.5966 (t0)
REVERT: A  949 LEU cc_start: 0.7370 (tt) cc_final: 0.6430 (mt)
REVERT: A  978 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7964 (mt-10)
  outliers start: 27
  outliers final: 20
  residues processed: 183
  average time/residue: 0.2251
  time to fit residues: 52.1454
Evaluate side-chains
  191 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  491 PHE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  579 SER
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  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 65 optimal weight:    0.0270
   chunk 67 optimal weight:    0.0870
   chunk 39 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.3816

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= 0.190
  Angle     :  0.641   9.519   8643  Z= 0.318
  Chirality :  0.042   0.191    966
  Planarity :  0.004   0.055   1042
  Dihedral  :  8.878  82.116    898
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 30.47 %
    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: -0.28 (0.33), residues: 722
  helix:  0.30 (0.28), residues: 362
  sheet: -1.24 (0.79), residues: 43
  loop : -0.47 (0.39), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 573 
 HIS   0.003   0.001   HIS A 585 
 PHE   0.016   0.001   PHE A 291 
 TYR   0.008   0.001   TYR A 785 
 ARG   0.007   0.001   ARG A 522 

*********************** 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
  189 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 GLU cc_start: 0.7222 (tp30) cc_final: 0.7004 (tp30)
REVERT: A  414 TYR cc_start: 0.8043 (t80) cc_final: 0.7598 (t80)
REVERT: A  425 ASN cc_start: 0.8267 (p0) cc_final: 0.8047 (t0)
REVERT: A  443 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: A  447 GLU cc_start: 0.8788 (tt0) cc_final: 0.8026 (tm-30)
REVERT: A  479 GLU cc_start: 0.6710 (tp30) cc_final: 0.6431 (tp30)
REVERT: A  505 LEU cc_start: 0.7750 (mp) cc_final: 0.7429 (mp)
REVERT: A  523 ASP cc_start: 0.7292 (p0) cc_final: 0.6933 (p0)
REVERT: A  536 MET cc_start: 0.7008 (ptp) cc_final: 0.6606 (ptp)
REVERT: A  539 ASP cc_start: 0.7919 (p0) cc_final: 0.7694 (p0)
REVERT: A  560 HIS cc_start: 0.7463 (t-90) cc_final: 0.6809 (t-90)
REVERT: A  578 LYS cc_start: 0.7759 (tttm) cc_final: 0.7374 (tttp)
REVERT: A  597 ILE cc_start: 0.7469 (mp) cc_final: 0.7064 (mm)
REVERT: A  607 LYS cc_start: 0.7837 (tppt) cc_final: 0.7299 (tmmt)
REVERT: A  651 PHE cc_start: 0.7439 (p90) cc_final: 0.6848 (p90)
REVERT: A  654 LYS cc_start: 0.7453 (mmtp) cc_final: 0.7219 (mptt)
REVERT: A  668 PHE cc_start: 0.8801 (t80) cc_final: 0.8596 (t80)
REVERT: A  672 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7940 (mm)
REVERT: A  673 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7140 (tm-30)
REVERT: A  710 ASN cc_start: 0.7513 (t0) cc_final: 0.7244 (t0)
REVERT: A  742 LEU cc_start: 0.8493 (tp) cc_final: 0.8254 (mp)
REVERT: A  746 ASN cc_start: 0.7596 (t0) cc_final: 0.7295 (p0)
REVERT: A  772 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6453 (mm110)
REVERT: A  790 LYS cc_start: 0.8807 (ptpp) cc_final: 0.8407 (ptpp)
REVERT: A  793 LYS cc_start: 0.8971 (mttt) cc_final: 0.8438 (mttt)
REVERT: A  804 CYS cc_start: 0.2740 (OUTLIER) cc_final: 0.1490 (p)
REVERT: A  815 MET cc_start: 0.5969 (tmm) cc_final: 0.5178 (tmm)
REVERT: A  820 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7690 (tptt)
REVERT: A  834 MET cc_start: 0.7012 (tmm) cc_final: 0.6365 (tmm)
REVERT: A  837 PHE cc_start: 0.8104 (m-80) cc_final: 0.7138 (m-80)
REVERT: A  876 LYS cc_start: 0.7839 (tptt) cc_final: 0.7626 (tptt)
REVERT: A  879 TYR cc_start: 0.8254 (t80) cc_final: 0.8009 (t80)
REVERT: A  939 ASN cc_start: 0.7044 (OUTLIER) cc_final: 0.6376 (t0)
REVERT: A  949 LEU cc_start: 0.7416 (tt) cc_final: 0.6493 (mt)
REVERT: A 1058 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7980 (ttmm)
  outliers start: 25
  outliers final: 19
  residues processed: 177
  average time/residue: 0.2121
  time to fit residues: 48.5403
Evaluate side-chains
  185 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
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  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  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 32 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    0.3980
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0040
   chunk 35 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0070
   chunk 61 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.3810

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 893 ASN
A 898 GLN
A 900 ASN
** 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: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
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= 0.192
  Angle     :  0.661  10.172   8643  Z= 0.327
  Chirality :  0.042   0.189    966
  Planarity :  0.004   0.055   1042
  Dihedral  :  8.832  81.826    898
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 30.92 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.28 (0.33), residues: 722
  helix:  0.29 (0.28), residues: 362
  sheet: -1.23 (0.79), residues: 43
  loop : -0.45 (0.39), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 573 
 HIS   0.003   0.001   HIS A 585 
 PHE   0.016   0.001   PHE A 291 
 TYR   0.007   0.001   TYR A 785 
 ARG   0.006   0.001   ARG A 631 

********************** 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
  183 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 GLN cc_start: 0.7187 (mp10) cc_final: 0.6891 (mp10)
REVERT: A  413 GLU cc_start: 0.7226 (tp30) cc_final: 0.6361 (tp30)
REVERT: A  414 TYR cc_start: 0.8043 (t80) cc_final: 0.7528 (t80)
REVERT: A  425 ASN cc_start: 0.8250 (p0) cc_final: 0.8039 (t0)
REVERT: A  443 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8346 (tm-30)
REVERT: A  447 GLU cc_start: 0.8791 (tt0) cc_final: 0.8021 (tm-30)
REVERT: A  479 GLU cc_start: 0.6726 (tp30) cc_final: 0.6318 (tp30)
REVERT: A  505 LEU cc_start: 0.7741 (mp) cc_final: 0.7431 (mp)
REVERT: A  511 GLU cc_start: 0.4830 (OUTLIER) cc_final: 0.3995 (tm-30)
REVERT: A  523 ASP cc_start: 0.7294 (p0) cc_final: 0.6930 (p0)
REVERT: A  536 MET cc_start: 0.7005 (ptp) cc_final: 0.6603 (ptp)
REVERT: A  539 ASP cc_start: 0.7881 (p0) cc_final: 0.7677 (p0)
REVERT: A  560 HIS cc_start: 0.7459 (t-90) cc_final: 0.6830 (t-90)
REVERT: A  578 LYS cc_start: 0.7761 (tttm) cc_final: 0.7400 (tttp)
REVERT: A  597 ILE cc_start: 0.7474 (mp) cc_final: 0.7074 (mm)
REVERT: A  607 LYS cc_start: 0.7811 (tppt) cc_final: 0.7568 (tppt)
REVERT: A  651 PHE cc_start: 0.7444 (p90) cc_final: 0.6859 (p90)
REVERT: A  654 LYS cc_start: 0.7461 (mmtp) cc_final: 0.7222 (mptt)
REVERT: A  672 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7970 (mm)
REVERT: A  673 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7141 (tm-30)
REVERT: A  710 ASN cc_start: 0.7544 (t0) cc_final: 0.7267 (t0)
REVERT: A  742 LEU cc_start: 0.8499 (tp) cc_final: 0.8255 (mp)
REVERT: A  746 ASN cc_start: 0.7566 (t0) cc_final: 0.7236 (p0)
REVERT: A  772 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6361 (mm110)
REVERT: A  790 LYS cc_start: 0.8808 (ptpp) cc_final: 0.8396 (ptpp)
REVERT: A  793 LYS cc_start: 0.8976 (mttt) cc_final: 0.8452 (mttt)
REVERT: A  804 CYS cc_start: 0.2743 (OUTLIER) cc_final: 0.1509 (p)
REVERT: A  815 MET cc_start: 0.5990 (tmm) cc_final: 0.5190 (tmm)
REVERT: A  820 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7684 (tptt)
REVERT: A  823 TYR cc_start: 0.8066 (t80) cc_final: 0.7485 (t80)
REVERT: A  834 MET cc_start: 0.7002 (tmm) cc_final: 0.6511 (tmm)
REVERT: A  876 LYS cc_start: 0.7837 (tptt) cc_final: 0.7629 (tptt)
REVERT: A  939 ASN cc_start: 0.7047 (OUTLIER) cc_final: 0.6390 (t0)
REVERT: A  949 LEU cc_start: 0.7472 (tt) cc_final: 0.6588 (mt)
  outliers start: 24
  outliers final: 19
  residues processed: 173
  average time/residue: 0.2259
  time to fit residues: 50.3543
Evaluate side-chains
  180 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
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  511 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  619 LYS
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  794 GLU
Chi-restraints excluded: chain A residue  800 LYS
Chi-restraints excluded: chain A residue  804 CYS
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  820 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue  954 THR
Chi-restraints excluded: chain A residue  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 53 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0670
   chunk 16 optimal weight:    0.0270
   chunk 58 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 50 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 41 optimal weight:    0.3980
   overall best weight:    0.2776

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.166256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.139842 restraints weight = 11429.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.144621 restraints weight = 6466.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.148080 restraints weight = 4233.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6477
moved from start:          0.4061

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= 0.193
  Angle     :  0.699  14.196   8643  Z= 0.350
  Chirality :  0.042   0.181    966
  Planarity :  0.004   0.057   1042
  Dihedral  :  8.805  81.526    898
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 30.32 %
    Favored  : 65.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.29 (0.28), residues: 355
  sheet: -1.17 (0.79), residues: 43
  loop : -0.38 (0.39), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 573 
 HIS   0.004   0.001   HIS A 417 
 PHE   0.016   0.001   PHE A 291 
 TYR   0.010   0.001   TYR A1054 
 ARG   0.006   0.001   ARG A 631 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1974.40 seconds
wall clock time: 47 minutes 12.69 seconds (2832.69 seconds total)