Starting phenix.real_space_refine
on Tue Sep 24 09:47:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/09_2024/6xos_22278.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/09_2024/6xos_22278.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/09_2024/6xos_22278.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/09_2024/6xos_22278.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/09_2024/6xos_22278.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/09_2024/6xos_22278.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4901      2.51       5
     N    1305      2.21       5
     O    1459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 7704
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7704
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7882
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
  Time building chain proxies: 8.03, per 1000 atoms: 1.04
  Number of scatterers: 7704
  At special positions: 0
  Unit cell: (82.176, 88.168, 95.016, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1459      8.00
     N    1305      7.00
     C    4901      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: 1.94
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1826

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      53.8% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 3.757A  pdb=" N   ARG A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 61
    Processing helix  chain 'A' and resid 101 through 110
    Processing helix  chain 'A' and resid 111 through 113
      No H-bonds generated for 'chain 'A' and resid 111 through 113'
    Processing helix  chain 'A' and resid 121 through 127
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.694A  pdb=" N   VAL A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.536A  pdb=" N   GLU A 244 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 284
      removed outlier: 3.916A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 288
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.643A  pdb=" N   ILE A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 457
      removed outlier: 4.685A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   HIS A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 481
      removed outlier: 3.585A  pdb=" N   ASN A 481 " --> pdb=" O   CYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 509 through 527
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 608 through 613
      removed outlier: 3.669A  pdb=" N   ARG A 612 " --> pdb=" O   GLU A 609 " (cutoff:3.500A)
      Proline residue:  A 613  - end of helix
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 631 through 642
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 695 through 713
      removed outlier: 3.618A  pdb=" N   PHE A 699 " --> pdb=" O   GLU A 695 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A 701 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
      removed outlier: 3.743A  pdb=" N   VAL A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 763 through 773
      removed outlier: 4.229A  pdb=" N   ARG A 767 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   HIS A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 878 through 894
      removed outlier: 4.407A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 901
    Processing helix  chain 'A' and resid 928 through 945
    Processing helix  chain 'A' and resid 948 through 964
    Processing helix  chain 'A' and resid 968 through 972
      removed outlier: 3.834A  pdb=" N   LYS A 972 " --> pdb=" O   PRO A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 979
      removed outlier: 3.987A  pdb=" N   PHE A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 996
    Processing helix  chain 'A' and resid 997 through 1008
    Processing helix  chain 'A' and resid 1025 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.856A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 134 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.856A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186
    Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313
      removed outlier: 3.516A  pdb=" N   CYS A 313 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   GLY A 392 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   PHE A 332 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   SER A 390 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   TYR A 388 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP A 336 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU A 386 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASP A 373 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313
      removed outlier: 3.516A  pdb=" N   CYS A 313 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   GLY A 392 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   PHE A 332 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   SER A 390 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   TYR A 388 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP A 336 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU A 386 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579
      removed outlier: 8.040A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 671 " --> pdb=" O   GLY A 645 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY A 645 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU A 673 " --> pdb=" O   THR A 643 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   THR A 643 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.550A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   ASN A 864 " --> pdb=" O   ARG A 924 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY A1022 " --> pdb=" O   PHE A 857 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LYS A 854 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   ARG A1037 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1342 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2439
        1.34 -     1.46: 1434
        1.46 -     1.57: 3961
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7896
  Sorted by residual:
  bond pdb=" CB  ASP A 165 "
       pdb=" CG  ASP A 165 "
    ideal  model  delta    sigma   weight residual
    1.516  1.461  0.055 2.50e-02 1.60e+03 4.81e+00
  bond pdb=" CG1 ILE A 432 "
       pdb=" CD1 ILE A 432 "
    ideal  model  delta    sigma   weight residual
    1.513  1.433  0.080 3.90e-02 6.57e+02 4.24e+00
  bond pdb=" CG  LEU A 736 "
       pdb=" CD2 LEU A 736 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.12e+00
  bond pdb=" CB  PRO A 103 "
       pdb=" CG  PRO A 103 "
    ideal  model  delta    sigma   weight residual
    1.492  1.405  0.087 5.00e-02 4.00e+02 3.03e+00
  bond pdb=" C   ILE A 242 "
       pdb=" N   PRO A 243 "
    ideal  model  delta    sigma   weight residual
    1.337  1.353 -0.017 9.80e-03 1.04e+04 2.94e+00
  ... (remaining 7891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10074
        2.09 -     4.17: 542
        4.17 -     6.26: 69
        6.26 -     8.34: 18
        8.34 -    10.43: 5
  Bond angle restraints: 10708
  Sorted by residual:
  angle pdb=" C   ALA A 580 "
        pdb=" N   GLY A 581 "
        pdb=" CA  GLY A 581 "
      ideal   model   delta    sigma   weight residual
     121.70  128.48   -6.78 1.80e+00 3.09e-01 1.42e+01
  angle pdb=" CA  PRO A 243 "
        pdb=" N   PRO A 243 "
        pdb=" CD  PRO A 243 "
      ideal   model   delta    sigma   weight residual
     112.00  106.95    5.05 1.40e+00 5.10e-01 1.30e+01
  angle pdb=" N   GLY A 581 "
        pdb=" CA  GLY A 581 "
        pdb=" C   GLY A 581 "
      ideal   model   delta    sigma   weight residual
     113.30  103.20   10.10 2.90e+00 1.19e-01 1.21e+01
  angle pdb=" C   HIS A 229 "
        pdb=" N   THR A 230 "
        pdb=" CA  THR A 230 "
      ideal   model   delta    sigma   weight residual
     120.63  126.16   -5.53 1.61e+00 3.86e-01 1.18e+01
  angle pdb=" C   ASP A 339 "
        pdb=" N   THR A 340 "
        pdb=" CA  THR A 340 "
      ideal   model   delta    sigma   weight residual
     120.54  124.96   -4.42 1.35e+00 5.49e-01 1.07e+01
  ... (remaining 10703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 4425
       17.76 -    35.52: 263
       35.52 -    53.28: 61
       53.28 -    71.04: 17
       71.04 -    88.80: 9
  Dihedral angle restraints: 4775
    sinusoidal: 1953
      harmonic: 2822
  Sorted by residual:
  dihedral pdb=" CA  PRO A 170 "
           pdb=" C   PRO A 170 "
           pdb=" N   CYS A 171 "
           pdb=" CA  CYS A 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.88   25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  PHE A 210 "
           pdb=" C   PHE A 210 "
           pdb=" N   THR A 211 "
           pdb=" CA  THR A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" C   ILE A 242 "
           pdb=" N   ILE A 242 "
           pdb=" CA  ILE A 242 "
           pdb=" CB  ILE A 242 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.59    9.59     0      2.50e+00 1.60e-01 1.47e+01
  ... (remaining 4772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 731
       0.053 -    0.106: 330
       0.106 -    0.159: 85
       0.159 -    0.212: 21
       0.212 -    0.265: 7
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CB  ILE A 242 "
            pdb=" CA  ILE A 242 "
            pdb=" CG1 ILE A 242 "
            pdb=" CG2 ILE A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CG  LEU A 895 "
            pdb=" CB  LEU A 895 "
            pdb=" CD1 LEU A 895 "
            pdb=" CD2 LEU A 895 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  VAL A1004 "
            pdb=" CA  VAL A1004 "
            pdb=" CG1 VAL A1004 "
            pdb=" CG2 VAL A1004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1171 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 899 "    0.018 2.00e-02 2.50e+03   3.50e-02 1.23e+01
        pdb=" C   ILE A 899 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ILE A 899 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ARG A 900 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A  34 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.71e+00
        pdb=" C   CYS A  34 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   CYS A  34 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU A  35 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 896 "    0.013 2.00e-02 2.50e+03   2.70e-02 7.27e+00
        pdb=" C   HIS A 896 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   HIS A 896 "    0.017 2.00e-02 2.50e+03
        pdb=" N   THR A 897 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1339
        2.76 -     3.30: 7122
        3.30 -     3.83: 12843
        3.83 -     4.37: 14940
        4.37 -     4.90: 26004
  Nonbonded interactions: 62248
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  98 "
            pdb=" OG1 THR A 100 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE1 GLN A 737 "
            pdb=" OG  SER A 741 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER A 190 "
            pdb=" OH  TYR A 538 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   SER A 351 "
            pdb=" OG  SER A 355 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" NH2 ARG A  36 "
            pdb=" O   ASN A 270 "
     model   vdw
     2.374 3.120
  ... (remaining 62243 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=0.42 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:             2.590
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.640
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
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      :  0.009   0.087   7896  Z= 0.567
  Angle     :  1.086  10.429  10708  Z= 0.593
  Chirality :  0.065   0.265   1174
  Planarity :  0.007   0.053   1398
  Dihedral  : 13.213  88.800   2949
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -1.45 (0.24), residues: 965
  helix: -1.12 (0.20), residues: 462
  sheet:  0.49 (0.36), residues: 174
  loop : -1.27 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 303 
 HIS   0.011   0.003   HIS A 186 
 PHE   0.026   0.003   PHE A 389 
 TYR   0.026   0.004   TYR A 258 
 ARG   0.006   0.001   ARG A  81 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 ARG cc_start: 0.8588 (mmp-170) cc_final: 0.8376 (mmm160)
REVERT: A  504 MET cc_start: 0.8109 (ttp) cc_final: 0.7886 (ttm)
REVERT: A  721 TYR cc_start: 0.8657 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  923 TYR cc_start: 0.7822 (t80) cc_final: 0.7255 (t80)
REVERT: A  928 THR cc_start: 0.8506 (p) cc_final: 0.8236 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2252
  time to fit residues: 38.4354
Evaluate side-chains
  79 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 72 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0270
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 151 GLN
A 204 ASN
** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 430 HIS
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 712 ASN
A 852 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7896  Z= 0.181
  Angle     :  0.673  13.338  10708  Z= 0.340
  Chirality :  0.044   0.254   1174
  Planarity :  0.005   0.044   1398
  Dihedral  :  4.286  19.568   1037
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  9.56 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.31 (0.27), residues: 965
  helix:  0.79 (0.24), residues: 468
  sheet:  0.46 (0.37), residues: 177
  loop : -0.68 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 998 
 PHE   0.012   0.001   PHE A 217 
 TYR   0.018   0.001   TYR A 450 
 ARG   0.006   0.001   ARG A 924 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8044 (m-10) cc_final: 0.7795 (m-10)
REVERT: A  721 TYR cc_start: 0.8689 (m-80) cc_final: 0.8296 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 98
  average time/residue: 0.1924
  time to fit residues: 26.4299
Evaluate side-chains
  77 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 94 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 698 HIS
A1016 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7896  Z= 0.292
  Angle     :  0.699   8.361  10708  Z= 0.351
  Chirality :  0.044   0.140   1174
  Planarity :  0.004   0.043   1398
  Dihedral  :  4.236  18.477   1037
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.77 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.72 (0.27), residues: 965
  helix:  1.22 (0.24), residues: 468
  sheet:  0.66 (0.37), residues: 182
  loop : -0.65 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 851 
 HIS   0.003   0.001   HIS A 719 
 PHE   0.014   0.002   PHE A 266 
 TYR   0.012   0.002   TYR A 268 
 ARG   0.005   0.001   ARG A 215 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8119 (m-10) cc_final: 0.7898 (m-10)
REVERT: A  721 TYR cc_start: 0.8757 (m-80) cc_final: 0.8330 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 75
  average time/residue: 0.1782
  time to fit residues: 19.3729
Evaluate side-chains
  66 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  778 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 25 optimal weight:    0.4980
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 486 GLN
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7896  Z= 0.178
  Angle     :  0.630   8.697  10708  Z= 0.310
  Chirality :  0.043   0.215   1174
  Planarity :  0.004   0.041   1398
  Dihedral  :  4.086  16.888   1037
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.59 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.98 (0.27), residues: 965
  helix:  1.46 (0.25), residues: 468
  sheet:  0.70 (0.37), residues: 180
  loop : -0.52 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 851 
 HIS   0.006   0.001   HIS A 108 
 PHE   0.012   0.001   PHE A 389 
 TYR   0.010   0.001   TYR A  76 
 ARG   0.006   0.000   ARG A 900 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8105 (m-10) cc_final: 0.7843 (m-10)
REVERT: A  721 TYR cc_start: 0.8721 (m-80) cc_final: 0.8287 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1820
  time to fit residues: 19.6474
Evaluate side-chains
  69 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 47 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    2.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7896  Z= 0.281
  Angle     :  0.664   9.667  10708  Z= 0.331
  Chirality :  0.044   0.144   1174
  Planarity :  0.004   0.041   1398
  Dihedral  :  4.152  17.462   1037
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.29 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.02 (0.28), residues: 965
  helix:  1.49 (0.25), residues: 469
  sheet:  0.63 (0.37), residues: 182
  loop : -0.46 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 851 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.023   0.002   PHE A 123 
 TYR   0.016   0.002   TYR A 923 
 ARG   0.008   0.001   ARG A 900 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8120 (m-10) cc_final: 0.7900 (m-10)
REVERT: A  206 MET cc_start: 0.7812 (mmt) cc_final: 0.7363 (mmt)
REVERT: A  721 TYR cc_start: 0.8747 (m-80) cc_final: 0.8269 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1753
  time to fit residues: 19.2085
Evaluate side-chains
  73 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  400 ASP
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  778 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 18 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 43 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7896  Z= 0.177
  Angle     :  0.650  10.397  10708  Z= 0.314
  Chirality :  0.044   0.242   1174
  Planarity :  0.004   0.039   1398
  Dihedral  :  4.044  17.524   1037
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.29 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.12 (0.28), residues: 965
  helix:  1.55 (0.25), residues: 470
  sheet:  0.65 (0.37), residues: 180
  loop : -0.34 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 851 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.010   0.001   PHE A 389 
 TYR   0.011   0.001   TYR A 587 
 ARG   0.008   0.000   ARG A 900 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8092 (m-10) cc_final: 0.7874 (m-10)
REVERT: A  206 MET cc_start: 0.7690 (mmt) cc_final: 0.7259 (mmt)
REVERT: A  721 TYR cc_start: 0.8744 (m-80) cc_final: 0.8232 (m-80)
REVERT: A  888 ARG cc_start: 0.8329 (tpp-160) cc_final: 0.8032 (tpt170)
  outliers start: 10
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1763
  time to fit residues: 19.0449
Evaluate side-chains
  70 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  778 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.0170
   chunk 52 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 92 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.1622

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7896  Z= 0.181
  Angle     :  0.658  10.915  10708  Z= 0.313
  Chirality :  0.043   0.162   1174
  Planarity :  0.004   0.039   1398
  Dihedral  :  3.956  17.535   1037
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.52 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.24 (0.28), residues: 965
  helix:  1.63 (0.25), residues: 470
  sheet:  0.68 (0.37), residues: 180
  loop : -0.23 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 851 
 HIS   0.005   0.001   HIS A 719 
 PHE   0.024   0.001   PHE A 123 
 TYR   0.016   0.001   TYR A 923 
 ARG   0.008   0.000   ARG A 900 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8164 (m-10) cc_final: 0.7945 (m-10)
REVERT: A  206 MET cc_start: 0.7694 (mmt) cc_final: 0.7061 (mmm)
REVERT: A  607 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7859 (tt)
REVERT: A  721 TYR cc_start: 0.8730 (m-80) cc_final: 0.8201 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1646
  time to fit residues: 18.0458
Evaluate side-chains
  71 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  607 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0000
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   chunk 84 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7896  Z= 0.172
  Angle     :  0.666  11.758  10708  Z= 0.319
  Chirality :  0.044   0.316   1174
  Planarity :  0.004   0.038   1398
  Dihedral  :  3.919  17.564   1037
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.99 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.33 (0.28), residues: 965
  helix:  1.66 (0.25), residues: 470
  sheet:  0.71 (0.37), residues: 180
  loop : -0.10 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 851 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.010   0.001   PHE A 389 
 TYR   0.009   0.001   TYR A 268 
 ARG   0.009   0.000   ARG A 900 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8132 (m-10) cc_final: 0.7928 (m-10)
REVERT: A  206 MET cc_start: 0.7674 (mmt) cc_final: 0.7350 (mmm)
REVERT: A  516 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8539 (tm-30)
REVERT: A  607 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7946 (tt)
REVERT: A  721 TYR cc_start: 0.8724 (m-80) cc_final: 0.8173 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 73
  average time/residue: 0.1786
  time to fit residues: 19.1222
Evaluate side-chains
  72 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  607 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 77 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   chunk 56 optimal weight:    0.4980
   chunk 91 optimal weight:    0.4980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7896  Z= 0.165
  Angle     :  0.675  11.886  10708  Z= 0.321
  Chirality :  0.044   0.295   1174
  Planarity :  0.004   0.037   1398
  Dihedral  :  3.855  16.188   1037
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 13.75 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.41 (0.28), residues: 965
  helix:  1.68 (0.25), residues: 472
  sheet:  0.76 (0.38), residues: 180
  loop :  0.02 (0.38), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 851 
 HIS   0.007   0.001   HIS A 104 
 PHE   0.024   0.001   PHE A 123 
 TYR   0.016   0.001   TYR A 923 
 ARG   0.009   0.000   ARG A 900 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.7435 (mmt) cc_final: 0.7050 (mmm)
REVERT: A  516 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8549 (tm-30)
REVERT: A  607 LEU cc_start: 0.8136 (tt) cc_final: 0.7808 (tt)
REVERT: A  721 TYR cc_start: 0.8734 (m-80) cc_final: 0.8211 (m-80)
  outliers start: 6
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1562
  time to fit residues: 18.1546
Evaluate side-chains
  73 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0370
   chunk 88 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7896  Z= 0.166
  Angle     :  0.703  12.294  10708  Z= 0.328
  Chirality :  0.044   0.318   1174
  Planarity :  0.004   0.037   1398
  Dihedral  :  3.824  16.202   1037
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 14.34 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.42 (0.28), residues: 965
  helix:  1.65 (0.25), residues: 472
  sheet:  0.75 (0.38), residues: 181
  loop :  0.09 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 851 
 HIS   0.007   0.001   HIS A 104 
 PHE   0.011   0.001   PHE A 389 
 TYR   0.009   0.001   TYR A 268 
 ARG   0.009   0.000   ARG A 900 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8530 (tm-30)
REVERT: A  607 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: A  721 TYR cc_start: 0.8756 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  789 MET cc_start: 0.8674 (mmm) cc_final: 0.8418 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1651
  time to fit residues: 18.8529
Evaluate side-chains
  75 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  607 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 70 optimal weight:    0.4980
   chunk 11 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0570
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.070588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.056880 restraints weight = 29406.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.059188 restraints weight = 14577.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.060775 restraints weight = 9060.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.3927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7896  Z= 0.167
  Angle     :  0.704  12.303  10708  Z= 0.330
  Chirality :  0.044   0.298   1174
  Planarity :  0.004   0.037   1398
  Dihedral  :  3.819  16.382   1037
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 15.62 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.44 (0.28), residues: 965
  helix:  1.68 (0.25), residues: 470
  sheet:  0.81 (0.38), residues: 180
  loop :  0.05 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 851 
 HIS   0.006   0.001   HIS A 104 
 PHE   0.024   0.001   PHE A 123 
 TYR   0.016   0.001   TYR A 923 
 ARG   0.009   0.000   ARG A 900 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1626.98 seconds
wall clock time: 30 minutes 0.70 seconds (1800.70 seconds total)