Starting phenix.real_space_refine
on Sun Apr  7 02:27:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/04_2024/8vxc_43616.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/04_2024/8vxc_43616.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/04_2024/8vxc_43616.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/04_2024/8vxc_43616.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/04_2024/8vxc_43616.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/04_2024/8vxc_43616.pdb"
  }
  resolution = 2.93
  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=   0.001 sd=   0.020
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      22      5.49       5
     S      27      5.16       5
     C    5857      2.51       5
     N    1678      2.21       5
     O    1806      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  928": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 9390
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 8946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1139, 8946
          Classifications: {'peptide': 1139}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 5, 'PTRANS': 44, 'TRANS': 1089}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 264
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
  Time building chain proxies: 5.57, per 1000 atoms: 0.59
  Number of scatterers: 9390
  At special positions: 0
  Unit cell: (85.855, 99.235, 112.615, 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      27     16.00
     P      22     15.00
     O    1806      8.00
     N    1678      7.00
     C    5857      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  - 3.50
        Amino acid           : False - 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: 4.26
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 3 sheets defined
      58.6% alpha, 7.6% beta
      4 base pairs and 15 stacking pairs defined.
    Time for finding SS restraints: 3.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
    Processing helix  chain 'A' and resid 11 through 16
    Processing helix  chain 'A' and resid 23 through 33
      removed outlier: 3.759A  pdb=" N   VAL A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 72
      removed outlier: 3.796A  pdb=" N   ALA A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG A  68 " --> pdb=" O   ASP A  64 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG A  70 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 95
      removed outlier: 3.532A  pdb=" N   ALA A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 118
      removed outlier: 3.622A  pdb=" N   PHE A 106 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   HIS A 107 " --> pdb=" O   ASP A 103 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   PHE A 108 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 129
    Processing helix  chain 'A' and resid 138 through 149
    Processing helix  chain 'A' and resid 151 through 166
      removed outlier: 3.636A  pdb=" N   ASP A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 224
    Processing helix  chain 'A' and resid 225 through 247
      removed outlier: 4.073A  pdb=" N   LEU A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 268
      removed outlier: 3.964A  pdb=" N   HIS A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
    Processing helix  chain 'A' and resid 285 through 299
      removed outlier: 3.682A  pdb=" N   GLU A 291 " --> pdb=" O   PRO A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 318
    Processing helix  chain 'A' and resid 330 through 333
    Processing helix  chain 'A' and resid 334 through 349
      removed outlier: 4.279A  pdb=" N   ILE A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 375
      removed outlier: 3.648A  pdb=" N   THR A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 400
      removed outlier: 3.671A  pdb=" N   ALA A 397 " --> pdb=" O   MET A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
      removed outlier: 3.683A  pdb=" N   PHE A 413 " --> pdb=" O   GLU A 409 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA A 414 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
      removed outlier: 3.611A  pdb=" N   ILE A 422 " --> pdb=" O   PRO A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 453
      removed outlier: 3.513A  pdb=" N   ARG A 444 " --> pdb=" O   GLU A 440 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   TYR A 445 " --> pdb=" O   ARG A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 461
      removed outlier: 6.180A  pdb=" N   ASP A 457 " --> pdb=" O   ARG A 454 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASP A 459 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 485
    Processing helix  chain 'A' and resid 553 through 568
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 3.908A  pdb=" N   VAL A 582 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   GLU A 583 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      Proline residue:  A 584  - end of helix
      removed outlier: 3.992A  pdb=" N   GLU A 587 " --> pdb=" O   GLU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
      removed outlier: 3.536A  pdb=" N   LEU A 609 " --> pdb=" O   PRO A 606 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 606 through 609'
    Processing helix  chain 'A' and resid 610 through 617
    Processing helix  chain 'A' and resid 624 through 633
    Processing helix  chain 'A' and resid 642 through 655
    Processing helix  chain 'A' and resid 691 through 701
      removed outlier: 3.644A  pdb=" N   ARG A 701 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 734
    Processing helix  chain 'A' and resid 742 through 760
    Processing helix  chain 'A' and resid 762 through 773
    Processing helix  chain 'A' and resid 788 through 813
      removed outlier: 4.166A  pdb=" N   ILE A 792 " --> pdb=" O   GLN A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 830
    Processing helix  chain 'A' and resid 833 through 840
    Processing helix  chain 'A' and resid 844 through 865
      removed outlier: 3.562A  pdb=" N   ARG A 848 " --> pdb=" O   ASP A 844 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 850 " --> pdb=" O   ASN A 846 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG A 865 " --> pdb=" O   TYR A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 878
    Processing helix  chain 'A' and resid 880 through 907
      removed outlier: 3.606A  pdb=" N   ALA A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ALA A 892 " --> pdb=" O   ASP A 888 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   LYS A 893 " --> pdb=" O   ALA A 889 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   GLN A 896 " --> pdb=" O   ALA A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 925
    Processing helix  chain 'A' and resid 938 through 948
    Processing helix  chain 'A' and resid 961 through 970
    Processing helix  chain 'A' and resid 973 through 990
    Processing helix  chain 'A' and resid 999 through 1003
    Processing helix  chain 'A' and resid 1007 through 1015
    Processing helix  chain 'A' and resid 1018 through 1028
      removed outlier: 3.702A  pdb=" N   GLY A1028 " --> pdb=" O   LEU A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1042
      removed outlier: 4.053A  pdb=" N   ILE A1036 " --> pdb=" O   ARG A1032 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LYS A1037 " --> pdb=" O   LEU A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1056
    Processing helix  chain 'A' and resid 1058 through 1063
      removed outlier: 3.528A  pdb=" N   ILE A1062 " --> pdb=" O   SER A1058 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1072 through 1079
      removed outlier: 4.201A  pdb=" N   VAL A1077 " --> pdb=" O   PRO A1073 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1085
    Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 382
      removed outlier: 6.357A  pdb=" N   SER A 382 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   VAL A 353 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ALA A 406 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   PHE A 355 " --> pdb=" O   ALA A 406 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   ARG A 352 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
      removed outlier: 8.731A  pdb=" N   ILE A 429 " --> pdb=" O   ARG A 352 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   VAL A 354 " --> pdb=" O   ILE A 429 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   ASP A 431 " --> pdb=" O   VAL A 354 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE A 356 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLY A 426 " --> pdb=" O   ARG A 462 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   VAL A 464 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   PHE A 428 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   LEU A 466 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   PHE A 430 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 526 through 531
      removed outlier: 6.204A  pdb=" N   SER A 527 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LEU A 515 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   GLY A 513 " --> pdb=" O   PHE A 529 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR A 715 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   VAL A 572 " --> pdb=" O   THR A 661 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   SER A 663 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   ILE A 574 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1100
      removed outlier: 8.507A  pdb=" N   LEU A1150 " --> pdb=" O   LEU A1118 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU A1118 " --> pdb=" O   LEU A1150 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   VAL A1152 " --> pdb=" O   LEU A1116 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1356 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      10 hydrogen bonds
      20 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      15 stacking parallelities
  Total time for adding SS restraints: 3.57

  Time building geometry restraints manager: 4.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2737
        1.33 -     1.45: 1545
        1.45 -     1.57: 5247
        1.57 -     1.69: 42
        1.69 -     1.81: 46
  Bond restraints: 9617
  Sorted by residual:
  bond pdb=" C   TYR A 575 "
       pdb=" N   CYS A 576 "
    ideal  model  delta    sigma   weight residual
    1.333  1.316  0.017 1.69e-02 3.50e+03 1.02e+00
  bond pdb=" C1'  DC B  12 "
       pdb=" N1   DC B  12 "
    ideal  model  delta    sigma   weight residual
    1.490  1.518 -0.028 3.00e-02 1.11e+03 8.97e-01
  bond pdb=" CA  MET A   1 "
       pdb=" C   MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 2.10e-02 2.27e+03 6.10e-01
  bond pdb=" C3'  DA C   8 "
       pdb=" C2'  DA C   8 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 2.00e-02 2.50e+03 6.09e-01
  bond pdb=" CB  TRP A 563 "
       pdb=" CG  TRP A 563 "
    ideal  model  delta    sigma   weight residual
    1.498  1.522 -0.024 3.10e-02 1.04e+03 5.96e-01
  ... (remaining 9612 not shown)

  Histogram of bond angle deviations from ideal:
       99.26 -   106.26: 365
      106.26 -   113.26: 5234
      113.26 -   120.26: 3535
      120.26 -   127.26: 3874
      127.26 -   134.26: 140
  Bond angle restraints: 13148
  Sorted by residual:
  angle pdb=" N   SER A 664 "
        pdb=" CA  SER A 664 "
        pdb=" C   SER A 664 "
      ideal   model   delta    sigma   weight residual
     110.07  103.16    6.91 1.46e+00 4.69e-01 2.24e+01
  angle pdb=" C   GLU A 923 "
        pdb=" N   VAL A 924 "
        pdb=" CA  VAL A 924 "
      ideal   model   delta    sigma   weight residual
     122.35  119.41    2.94 1.18e+00 7.18e-01 6.22e+00
  angle pdb=" N   THR A 666 "
        pdb=" CA  THR A 666 "
        pdb=" C   THR A 666 "
      ideal   model   delta    sigma   weight residual
     113.16  110.20    2.96 1.24e+00 6.50e-01 5.69e+00
  angle pdb=" N   SER A 664 "
        pdb=" CA  SER A 664 "
        pdb=" CB  SER A 664 "
      ideal   model   delta    sigma   weight residual
     109.55  112.30   -2.75 1.30e+00 5.92e-01 4.47e+00
  angle pdb=" N   VAL A 955 "
        pdb=" CA  VAL A 955 "
        pdb=" C   VAL A 955 "
      ideal   model   delta    sigma   weight residual
     109.34  104.99    4.35 2.08e+00 2.31e-01 4.36e+00
  ... (remaining 13143 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5194
       17.97 -    35.95: 385
       35.95 -    53.92: 110
       53.92 -    71.90: 40
       71.90 -    89.87: 5
  Dihedral angle restraints: 5734
    sinusoidal: 2453
      harmonic: 3281
  Sorted by residual:
  dihedral pdb=" CA  PRO A 665 "
           pdb=" C   PRO A 665 "
           pdb=" N   THR A 666 "
           pdb=" CA  THR A 666 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.87   18.13     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  PRO A 541 "
           pdb=" C   PRO A 541 "
           pdb=" N   ASN A 542 "
           pdb=" CA  ASN A 542 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.91  -17.09     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ALA A   5 "
           pdb=" C   ALA A   5 "
           pdb=" N   ASP A   6 "
           pdb=" CA  ASP A   6 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.84  -15.16     0      5.00e+00 4.00e-02 9.19e+00
  ... (remaining 5731 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 947
       0.030 -    0.060: 375
       0.060 -    0.090: 98
       0.090 -    0.120: 60
       0.120 -    0.150: 13
  Chirality restraints: 1493
  Sorted by residual:
  chirality pdb=" CA  VAL A 955 "
            pdb=" N   VAL A 955 "
            pdb=" C   VAL A 955 "
            pdb=" CB  VAL A 955 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  TRP A 563 "
            pdb=" N   TRP A 563 "
            pdb=" C   TRP A 563 "
            pdb=" CB  TRP A 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" CA  ILE A1138 "
            pdb=" N   ILE A1138 "
            pdb=" C   ILE A1138 "
            pdb=" CB  ILE A1138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 1490 not shown)

  Planarity restraints: 1636
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 535 "   -0.036 5.00e-02 4.00e+02   5.39e-02 4.65e+00
        pdb=" N   PRO A 536 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 536 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 536 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 534 "   -0.033 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO A 535 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 375 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO A 376 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 376 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 376 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1633 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 910
        2.74 -     3.28: 9555
        3.28 -     3.82: 16371
        3.82 -     4.36: 19477
        4.36 -     4.90: 32531
  Nonbonded interactions: 78844
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 454 "
            pdb=" O   ASP A 828 "
     model   vdw
     2.206 2.520
  nonbonded pdb=" NH2 ARG A 595 "
            pdb=" OP1  DT B   4 "
     model   vdw
     2.215 2.520
  nonbonded pdb=" O   PHE A 413 "
            pdb=" ND2 ASN A 417 "
     model   vdw
     2.255 2.520
  nonbonded pdb=" OG1 THR A1014 "
            pdb=" OG  SER A1022 "
     model   vdw
     2.271 2.440
  nonbonded pdb=" O   ARG A 360 "
            pdb=" OG  SER A 363 "
     model   vdw
     2.276 2.440
  ... (remaining 78839 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          3.910
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     32.480
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:12.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
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   0.028   9617  Z= 0.164
  Angle     :  0.507   6.909  13148  Z= 0.284
  Chirality :  0.039   0.150   1493
  Planarity :  0.004   0.054   1636
  Dihedral  : 14.757  89.872   3614
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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 (0.25), residues: 1135
  helix:  0.86 (0.22), residues: 590
  sheet: -0.28 (0.55), residues: 98
  loop : -0.56 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A  35 
 HIS   0.009   0.001   HIS A 756 
 PHE   0.015   0.001   PHE A 925 
 TYR   0.021   0.001   TYR A 645 
 ARG   0.003   0.000   ARG A 646 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7427 (tpp) cc_final: 0.7090 (mmt)
REVERT: A  336 THR cc_start: 0.7888 (m) cc_final: 0.7515 (m)
REVERT: A  394 ASP cc_start: 0.6899 (m-30) cc_final: 0.6627 (m-30)
REVERT: A  448 GLN cc_start: 0.8273 (tt0) cc_final: 0.8045 (tt0)
REVERT: A  637 HIS cc_start: 0.7948 (t-90) cc_final: 0.7737 (t-170)
REVERT: A  692 VAL cc_start: 0.7445 (p) cc_final: 0.7071 (t)
REVERT: A  863 TRP cc_start: 0.7715 (m100) cc_final: 0.6802 (m-10)
REVERT: A  928 TYR cc_start: 0.8426 (t80) cc_final: 0.8172 (t80)
REVERT: A 1048 SER cc_start: 0.7645 (t) cc_final: 0.7110 (p)
REVERT: A 1051 GLU cc_start: 0.7145 (mp0) cc_final: 0.6653 (mp0)
REVERT: A 1078 MET cc_start: 0.3555 (ttt) cc_final: 0.3306 (ttt)
REVERT: A 1098 ARG cc_start: 0.6652 (ttt90) cc_final: 0.6342 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 1.3490
  time to fit residues: 277.9656
Evaluate side-chains
  150 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0870
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
A 821 GLN
A 989 ASN
A1064 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9617  Z= 0.237
  Angle     :  0.548   6.301  13148  Z= 0.291
  Chirality :  0.041   0.151   1493
  Planarity :  0.005   0.052   1636
  Dihedral  : 14.379  74.447   1498
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 12.13 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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 (0.25), residues: 1135
  helix:  0.89 (0.22), residues: 596
  sheet: -0.17 (0.54), residues: 106
  loop : -0.71 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 266 
 HIS   0.009   0.001   HIS A 756 
 PHE   0.014   0.002   PHE A 106 
 TYR   0.015   0.002   TYR A 445 
 ARG   0.005   0.000   ARG A 944 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7380 (tpp) cc_final: 0.7036 (mmt)
REVERT: A  448 GLN cc_start: 0.8283 (tt0) cc_final: 0.8003 (tt0)
REVERT: A  637 HIS cc_start: 0.7895 (t-90) cc_final: 0.7645 (t-90)
REVERT: A  863 TRP cc_start: 0.7807 (m100) cc_final: 0.6867 (m-10)
REVERT: A 1048 SER cc_start: 0.7605 (t) cc_final: 0.7248 (p)
REVERT: A 1078 MET cc_start: 0.3528 (ttt) cc_final: 0.3284 (ttt)
  outliers start: 22
  outliers final: 8
  residues processed: 172
  average time/residue: 1.4394
  time to fit residues: 263.0489
Evaluate side-chains
  158 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  614 SER
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue 1020 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 86 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 104 optimal weight:    0.0770
   chunk 113 optimal weight:    0.6980
   chunk 93 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 83 optimal weight:    0.3980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 365 GLN
A 502 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9617  Z= 0.226
  Angle     :  0.534   6.955  13148  Z= 0.281
  Chirality :  0.041   0.157   1493
  Planarity :  0.005   0.052   1636
  Dihedral  : 14.247  75.611   1498
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.66 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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 (0.25), residues: 1135
  helix:  0.98 (0.22), residues: 592
  sheet: -0.14 (0.54), residues: 106
  loop : -0.85 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  35 
 HIS   0.005   0.001   HIS A 756 
 PHE   0.012   0.002   PHE A 106 
 TYR   0.027   0.002   TYR A1165 
 ARG   0.006   0.000   ARG A 944 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7364 (tpp) cc_final: 0.7030 (mmt)
REVERT: A  411 LEU cc_start: 0.7519 (tp) cc_final: 0.7309 (tt)
REVERT: A  448 GLN cc_start: 0.8278 (tt0) cc_final: 0.8002 (tt0)
REVERT: A  637 HIS cc_start: 0.7876 (t-90) cc_final: 0.7665 (t-90)
REVERT: A  796 ILE cc_start: 0.7995 (pt) cc_final: 0.7795 (OUTLIER)
REVERT: A  863 TRP cc_start: 0.7801 (m100) cc_final: 0.6804 (m-10)
REVERT: A  963 THR cc_start: 0.7207 (t) cc_final: 0.6973 (m)
REVERT: A 1048 SER cc_start: 0.7726 (t) cc_final: 0.7323 (p)
REVERT: A 1078 MET cc_start: 0.3526 (ttt) cc_final: 0.3291 (ttt)
  outliers start: 20
  outliers final: 10
  residues processed: 165
  average time/residue: 1.3854
  time to fit residues: 243.7626
Evaluate side-chains
  160 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue 1020 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 111 optimal weight:    0.2980
   chunk 99 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 365 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1064 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   9617  Z= 0.367
  Angle     :  0.603   7.253  13148  Z= 0.318
  Chirality :  0.044   0.178   1493
  Planarity :  0.005   0.059   1636
  Dihedral  : 14.276  77.047   1498
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.30 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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: -0.01 (0.25), residues: 1135
  helix:  0.78 (0.22), residues: 593
  sheet: -0.43 (0.54), residues: 104
  loop : -0.91 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  35 
 HIS   0.006   0.001   HIS A 116 
 PHE   0.015   0.002   PHE A 106 
 TYR   0.024   0.003   TYR A 928 
 ARG   0.011   0.001   ARG A 156 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.6756 (mtm) cc_final: 0.6552 (mtt)
REVERT: A  261 LEU cc_start: 0.6036 (tp) cc_final: 0.5672 (tt)
REVERT: A  367 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6596 (tp30)
REVERT: A  448 GLN cc_start: 0.8259 (tt0) cc_final: 0.8001 (tt0)
REVERT: A  637 HIS cc_start: 0.7950 (t-90) cc_final: 0.7712 (t-90)
REVERT: A  796 ILE cc_start: 0.8018 (pt) cc_final: 0.7755 (OUTLIER)
REVERT: A  863 TRP cc_start: 0.7872 (m100) cc_final: 0.6879 (m100)
REVERT: A 1048 SER cc_start: 0.7743 (t) cc_final: 0.7346 (p)
REVERT: A 1078 MET cc_start: 0.3692 (ttt) cc_final: 0.3445 (ttt)
REVERT: A 1151 ARG cc_start: 0.6966 (mtp-110) cc_final: 0.6728 (mtp180)
REVERT: A 1162 MET cc_start: 0.6997 (tmm) cc_final: 0.6724 (tmm)
  outliers start: 27
  outliers final: 15
  residues processed: 184
  average time/residue: 1.3258
  time to fit residues: 260.0704
Evaluate side-chains
  172 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  502 GLN
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  821 GLN
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue 1020 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0970
   chunk 0 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 365 GLN
A 502 GLN
A 800 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9617  Z= 0.206
  Angle     :  0.545   7.882  13148  Z= 0.287
  Chirality :  0.040   0.171   1493
  Planarity :  0.005   0.056   1636
  Dihedral  : 14.044  75.084   1498
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.83 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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:  0.22 (0.26), residues: 1135
  helix:  0.98 (0.22), residues: 599
  sheet: -0.21 (0.57), residues: 98
  loop : -0.88 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 266 
 HIS   0.004   0.001   HIS A 116 
 PHE   0.026   0.002   PHE A 106 
 TYR   0.025   0.002   TYR A 928 
 ARG   0.009   0.000   ARG A 944 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  448 GLN cc_start: 0.8269 (tt0) cc_final: 0.7999 (tt0)
REVERT: A  502 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6314 (mt0)
REVERT: A  637 HIS cc_start: 0.7852 (t-90) cc_final: 0.7649 (t-90)
REVERT: A  863 TRP cc_start: 0.7828 (m100) cc_final: 0.6859 (m-10)
REVERT: A  963 THR cc_start: 0.7103 (t) cc_final: 0.6898 (m)
REVERT: A 1048 SER cc_start: 0.7665 (t) cc_final: 0.7273 (p)
REVERT: A 1078 MET cc_start: 0.3644 (ttt) cc_final: 0.3405 (ttt)
  outliers start: 24
  outliers final: 11
  residues processed: 173
  average time/residue: 1.3508
  time to fit residues: 249.2275
Evaluate side-chains
  161 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  502 GLN
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  821 GLN
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue 1020 SER
Chi-restraints excluded: chain A residue 1067 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
A 502 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 989 ASN
A1050 GLN
A1064 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9617  Z= 0.298
  Angle     :  0.579   8.625  13148  Z= 0.303
  Chirality :  0.042   0.178   1493
  Planarity :  0.005   0.058   1636
  Dihedral  : 14.058  74.931   1498
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 18.78 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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:  0.10 (0.25), residues: 1135
  helix:  0.91 (0.22), residues: 599
  sheet: -0.27 (0.57), residues: 98
  loop : -0.97 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 266 
 HIS   0.004   0.001   HIS A 638 
 PHE   0.022   0.002   PHE A 106 
 TYR   0.029   0.002   TYR A1165 
 ARG   0.007   0.001   ARG A 156 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  367 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6592 (tp30)
REVERT: A  448 GLN cc_start: 0.8267 (tt0) cc_final: 0.7964 (tt0)
REVERT: A  796 ILE cc_start: 0.8021 (pt) cc_final: 0.7805 (OUTLIER)
REVERT: A  863 TRP cc_start: 0.7887 (m100) cc_final: 0.6845 (m100)
REVERT: A  924 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7217 (t)
REVERT: A 1048 SER cc_start: 0.7732 (t) cc_final: 0.7320 (p)
REVERT: A 1076 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7830 (tpt90)
REVERT: A 1078 MET cc_start: 0.3651 (ttt) cc_final: 0.3425 (ttt)
  outliers start: 25
  outliers final: 13
  residues processed: 170
  average time/residue: 1.3765
  time to fit residues: 249.4484
Evaluate side-chains
  162 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue 1020 SER
Chi-restraints excluded: chain A residue 1076 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 68 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
A 400 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9617  Z= 0.271
  Angle     :  0.576   9.369  13148  Z= 0.300
  Chirality :  0.042   0.170   1493
  Planarity :  0.005   0.058   1636
  Dihedral  : 13.981  73.556   1498
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.20 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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:  0.12 (0.25), residues: 1135
  helix:  0.93 (0.22), residues: 600
  sheet: -0.28 (0.58), residues: 98
  loop : -0.96 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 266 
 HIS   0.005   0.001   HIS A 116 
 PHE   0.032   0.002   PHE A 106 
 TYR   0.029   0.002   TYR A 928 
 ARG   0.005   0.000   ARG A 156 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  367 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6603 (tp30)
REVERT: A  448 GLN cc_start: 0.8262 (tt0) cc_final: 0.7958 (tt0)
REVERT: A  699 ILE cc_start: 0.8326 (pt) cc_final: 0.8097 (pt)
REVERT: A  740 MET cc_start: 0.7950 (mmp) cc_final: 0.7726 (mmt)
REVERT: A  842 TYR cc_start: 0.7505 (m-10) cc_final: 0.7036 (m-80)
REVERT: A  863 TRP cc_start: 0.7888 (m100) cc_final: 0.6829 (m-10)
REVERT: A  924 VAL cc_start: 0.7522 (OUTLIER) cc_final: 0.7251 (t)
REVERT: A  944 ARG cc_start: 0.7851 (tpt-90) cc_final: 0.7630 (tpt-90)
REVERT: A 1048 SER cc_start: 0.7724 (t) cc_final: 0.7331 (p)
REVERT: A 1076 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7852 (tpt90)
REVERT: A 1078 MET cc_start: 0.3636 (ttt) cc_final: 0.3410 (ttt)
REVERT: A 1162 MET cc_start: 0.6862 (tmm) cc_final: 0.6476 (tmm)
  outliers start: 25
  outliers final: 18
  residues processed: 168
  average time/residue: 1.3627
  time to fit residues: 244.2466
Evaluate side-chains
  166 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1020 SER
Chi-restraints excluded: chain A residue 1067 ASN
Chi-restraints excluded: chain A residue 1076 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 75 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0170
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 989 ASN
A1064 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9617  Z= 0.219
  Angle     :  0.569  10.051  13148  Z= 0.294
  Chirality :  0.041   0.158   1493
  Planarity :  0.005   0.071   1636
  Dihedral  : 13.883  73.471   1498
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.15 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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:  0.27 (0.26), residues: 1135
  helix:  0.98 (0.22), residues: 607
  sheet: -0.10 (0.58), residues: 100
  loop : -0.84 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 266 
 HIS   0.004   0.001   HIS A1064 
 PHE   0.028   0.002   PHE A 106 
 TYR   0.031   0.002   TYR A 928 
 ARG   0.007   0.000   ARG A 696 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  448 GLN cc_start: 0.8269 (tt0) cc_final: 0.7955 (tt0)
REVERT: A  500 ARG cc_start: 0.7334 (ttp-110) cc_final: 0.7036 (ttp-170)
REVERT: A  699 ILE cc_start: 0.8257 (pt) cc_final: 0.8037 (pt)
REVERT: A  842 TYR cc_start: 0.7372 (m-10) cc_final: 0.6962 (m-80)
REVERT: A  863 TRP cc_start: 0.7872 (m100) cc_final: 0.6847 (m-10)
REVERT: A  924 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7202 (t)
REVERT: A  944 ARG cc_start: 0.7874 (tpt-90) cc_final: 0.7644 (tpt-90)
REVERT: A 1016 THR cc_start: 0.7555 (p) cc_final: 0.7299 (p)
REVERT: A 1048 SER cc_start: 0.7699 (t) cc_final: 0.7299 (p)
REVERT: A 1076 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7850 (tpt90)
REVERT: A 1078 MET cc_start: 0.3616 (ttt) cc_final: 0.3378 (ttt)
  outliers start: 26
  outliers final: 17
  residues processed: 168
  average time/residue: 1.3293
  time to fit residues: 238.3601
Evaluate side-chains
  166 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  968 GLU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1020 SER
Chi-restraints excluded: chain A residue 1067 ASN
Chi-restraints excluded: chain A residue 1076 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0670
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 989 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9617  Z= 0.271
  Angle     :  0.601  11.230  13148  Z= 0.313
  Chirality :  0.042   0.204   1493
  Planarity :  0.005   0.077   1636
  Dihedral  : 13.894  73.117   1498
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 21.10 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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:  0.16 (0.26), residues: 1135
  helix:  0.89 (0.22), residues: 607
  sheet: -0.23 (0.58), residues: 100
  loop : -0.86 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 266 
 HIS   0.004   0.001   HIS A 116 
 PHE   0.028   0.002   PHE A 106 
 TYR   0.033   0.002   TYR A 928 
 ARG   0.006   0.000   ARG A 156 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7015 (tpp) cc_final: 0.6729 (tpp)
REVERT: A  147 LEU cc_start: 0.8463 (tp) cc_final: 0.8211 (mt)
REVERT: A  266 TRP cc_start: 0.6549 (t-100) cc_final: 0.6215 (t-100)
REVERT: A  448 GLN cc_start: 0.8267 (tt0) cc_final: 0.7956 (tt0)
REVERT: A  842 TYR cc_start: 0.7398 (m-10) cc_final: 0.6880 (m-80)
REVERT: A  863 TRP cc_start: 0.7895 (m100) cc_final: 0.6883 (m-10)
REVERT: A  924 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7218 (t)
REVERT: A  944 ARG cc_start: 0.7876 (tpt-90) cc_final: 0.7632 (tpt-90)
REVERT: A 1048 SER cc_start: 0.7717 (t) cc_final: 0.7310 (p)
REVERT: A 1076 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7854 (tpt90)
REVERT: A 1078 MET cc_start: 0.3607 (ttt) cc_final: 0.3406 (ttt)
  outliers start: 23
  outliers final: 18
  residues processed: 161
  average time/residue: 1.3342
  time to fit residues: 229.2319
Evaluate side-chains
  168 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  587 GLU
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  821 GLN
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  968 GLU
Chi-restraints excluded: chain A residue 1020 SER
Chi-restraints excluded: chain A residue 1067 ASN
Chi-restraints excluded: chain A residue 1076 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0970
   chunk 114 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   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 365 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9617  Z= 0.257
  Angle     :  0.604  11.088  13148  Z= 0.314
  Chirality :  0.042   0.193   1493
  Planarity :  0.005   0.076   1636
  Dihedral  : 13.869  72.416   1498
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.73 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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:  0.16 (0.26), residues: 1135
  helix:  0.91 (0.22), residues: 602
  sheet: -0.17 (0.58), residues: 100
  loop : -0.88 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 266 
 HIS   0.010   0.001   HIS A1064 
 PHE   0.016   0.002   PHE A 106 
 TYR   0.035   0.002   TYR A 928 
 ARG   0.007   0.000   ARG A 156 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LEU cc_start: 0.8470 (tp) cc_final: 0.8230 (mt)
REVERT: A  264 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6737 (t0)
REVERT: A  387 SER cc_start: 0.8496 (t) cc_final: 0.8271 (t)
REVERT: A  448 GLN cc_start: 0.8263 (tt0) cc_final: 0.7949 (tt0)
REVERT: A  500 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7352 (ttp-170)
REVERT: A  842 TYR cc_start: 0.7292 (m-80) cc_final: 0.6837 (m-80)
REVERT: A  863 TRP cc_start: 0.7893 (m100) cc_final: 0.6888 (m-10)
REVERT: A  924 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.7165 (t)
REVERT: A  944 ARG cc_start: 0.7871 (tpt-90) cc_final: 0.7636 (tpt-90)
REVERT: A 1048 SER cc_start: 0.7713 (t) cc_final: 0.7301 (p)
REVERT: A 1076 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7791 (tpt90)
REVERT: A 1162 MET cc_start: 0.7088 (tmm) cc_final: 0.6660 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 164
  average time/residue: 1.3487
  time to fit residues: 235.6971
Evaluate side-chains
  164 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  459 ASP
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  587 GLU
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  968 GLU
Chi-restraints excluded: chain A residue 1020 SER
Chi-restraints excluded: chain A residue 1067 ASN
Chi-restraints excluded: chain A residue 1076 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0050
   chunk 91 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 93 optimal weight:    0.0370
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.3272

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 GLN
A 989 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.167883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.152305 restraints weight = 12549.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 1.78
r_work: 0.3902 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3755 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9617  Z= 0.200
  Angle     :  0.589  11.712  13148  Z= 0.305
  Chirality :  0.041   0.204   1493
  Planarity :  0.005   0.062   1636
  Dihedral  : 13.775  72.629   1498
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 22.57 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    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:  0.29 (0.26), residues: 1135
  helix:  1.00 (0.22), residues: 602
  sheet: -0.02 (0.59), residues: 100
  loop : -0.84 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1094 
 HIS   0.010   0.001   HIS A1064 
 PHE   0.017   0.002   PHE A 106 
 TYR   0.036   0.002   TYR A 928 
 ARG   0.005   0.000   ARG A 156 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4311.17 seconds
wall clock time: 77 minutes 44.12 seconds (4664.12 seconds total)