Starting phenix.real_space_refine
on Mon Sep 23 23:06:10 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/09_2024/7dcp_30638.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/09_2024/7dcp_30638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/09_2024/7dcp_30638.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/09_2024/7dcp_30638.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/09_2024/7dcp_30638.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/09_2024/7dcp_30638.cif"
  }
  resolution = 3.15
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 168 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      35      5.16       5
     C    3741      2.51       5
     N    1001      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 5868
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "x"
      Number of atoms: 5355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 670, 5355
          Classifications: {'peptide': 670}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 636}
          Chain breaks: 2
    Chain: "y"
      Number of atoms: 485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 485
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 57}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "x"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.34, per 1000 atoms: 0.74
  Number of scatterers: 5868
  At special positions: 0
  Unit cell: (92.75, 90.7625, 83.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      35     16.00
     P       2     15.00
     Mg      1     11.99
     O    1088      8.00
     N    1001      7.00
     C    3741      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: 1.36
  Conformation dependent library (CDL) restraints added in 763.8 milliseconds
  

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1382

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      51.0% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'x' and resid 12 through 16
      removed outlier: 3.774A  pdb=" N   THR x  16 " --> pdb=" O   VAL x  13 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 216 through 222
      removed outlier: 3.720A  pdb=" N   ARG x 220 " --> pdb=" O   ILE x 216 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS x 221 " --> pdb=" O   GLN x 217 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU x 222 " --> pdb=" O   GLU x 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'x' and resid 216 through 222'
    Processing helix  chain 'x' and resid 228 through 239
      removed outlier: 3.515A  pdb=" N   GLN x 234 " --> pdb=" O   ASP x 230 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 251 through 264
      removed outlier: 3.573A  pdb=" N   LEU x 256 " --> pdb=" O   LYS x 252 " (cutoff:3.500A)
      Proline residue:  x 257  - end of helix
    Processing helix  chain 'x' and resid 279 through 295
      removed outlier: 3.584A  pdb=" N   VAL x 286 " --> pdb=" O   ALA x 282 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA x 287 " --> pdb=" O   ALA x 283 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 324 through 334
      removed outlier: 3.759A  pdb=" N   LEU x 328 " --> pdb=" O   ASP x 324 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE x 331 " --> pdb=" O   LEU x 327 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU x 332 " --> pdb=" O   LEU x 328 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   THR x 333 " --> pdb=" O   ARG x 329 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 348 through 351
    Processing helix  chain 'x' and resid 352 through 369
      removed outlier: 3.736A  pdb=" N   ASP x 364 " --> pdb=" O   GLY x 360 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE x 365 " --> pdb=" O   LEU x 361 " (cutoff:3.500A)
      Proline residue:  x 367  - end of helix
    Processing helix  chain 'x' and resid 383 through 390
    Processing helix  chain 'x' and resid 416 through 432
      removed outlier: 3.628A  pdb=" N   THR x 431 " --> pdb=" O   GLN x 427 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 444 through 463
    Processing helix  chain 'x' and resid 479 through 484
      removed outlier: 3.773A  pdb=" N   LEU x 484 " --> pdb=" O   GLN x 480 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 502 through 507
      removed outlier: 3.875A  pdb=" N   THR x 506 " --> pdb=" O   ASN x 502 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 542 through 551
    Processing helix  chain 'x' and resid 552 through 555
      removed outlier: 3.843A  pdb=" N   ARG x 555 " --> pdb=" O   ARG x 552 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'x' and resid 552 through 555'
    Processing helix  chain 'x' and resid 567 through 572
      removed outlier: 3.675A  pdb=" N   HIS x 572 " --> pdb=" O   TRP x 568 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 580 through 584
    Processing helix  chain 'x' and resid 587 through 598
    Processing helix  chain 'x' and resid 612 through 626
    Processing helix  chain 'x' and resid 636 through 643
    Processing helix  chain 'x' and resid 648 through 661
      removed outlier: 3.602A  pdb=" N   ALA x 659 " --> pdb=" O   LEU x 655 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 667 through 680
      removed outlier: 3.605A  pdb=" N   THR x 673 " --> pdb=" O   GLU x 669 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   HIS x 679 " --> pdb=" O   VAL x 675 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLU x 680 " --> pdb=" O   SER x 676 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 681 through 684
    Processing helix  chain 'x' and resid 688 through 697
      removed outlier: 3.766A  pdb=" N   ALA x 692 " --> pdb=" O   GLN x 688 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER x 695 " --> pdb=" O   ASP x 691 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 702 through 717
      removed outlier: 3.536A  pdb=" N   PHE x 711 " --> pdb=" O   TYR x 707 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 720 through 728
      removed outlier: 3.919A  pdb=" N   CYS x 724 " --> pdb=" O   SER x 720 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN x 725 " --> pdb=" O   ARG x 721 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 730 through 752
      removed outlier: 3.646A  pdb=" N   ARG x 736 " --> pdb=" O   LYS x 732 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 752 through 765
      removed outlier: 3.501A  pdb=" N   LYS x 763 " --> pdb=" O   GLN x 759 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY x 765 " --> pdb=" O   ARG x 761 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 767 through 783
      removed outlier: 4.015A  pdb=" N   ASN x 772 " --> pdb=" O   ALA x 768 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ALA x 773 " --> pdb=" O   GLY x 769 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 813 through 822
      removed outlier: 3.518A  pdb=" N   VAL x 817 " --> pdb=" O   SER x 813 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 852 through 859
      removed outlier: 3.872A  pdb=" N   ILE x 856 " --> pdb=" O   GLU x 852 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 859 through 867
      removed outlier: 5.709A  pdb=" N   ASP x 865 " --> pdb=" O   GLN x 861 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU x 866 " --> pdb=" O   ILE x 862 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 95 through 100
    Processing helix  chain 'y' and resid 101 through 114
      removed outlier: 3.779A  pdb=" N   GLY y 106 " --> pdb=" O   VAL y 102 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ASP y 107 " --> pdb=" O   GLU y 103 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY y 112 " --> pdb=" O   ALA y 108 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'x' and resid 171 through 172
      removed outlier: 5.572A  pdb=" N   TYR x 171 " --> pdb=" O   VAL y 167 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'x' and resid 310 through 311
      removed outlier: 6.270A  pdb=" N   ILE x 273 " --> pdb=" O   LYS x 320 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   MET x 322 " --> pdb=" O   ILE x 273 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ILE x 275 " --> pdb=" O   MET x 322 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN x 272 " --> pdb=" O   TYR x 340 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   CYS x 342 " --> pdb=" O   GLN x 272 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   SER x 341 " --> pdb=" O   LYS x 373 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   LEU x 375 " --> pdb=" O   SER x 341 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ILE x 343 " --> pdb=" O   LEU x 375 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   SER x 377 " --> pdb=" O   ILE x 343 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE x 345 " --> pdb=" O   SER x 377 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   PHE x 396 " --> pdb=" O   VAL x 241 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ILE x 243 " --> pdb=" O   PHE x 396 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   VAL x 398 " --> pdb=" O   ILE x 243 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   MET x 245 " --> pdb=" O   VAL x 398 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'x' and resid 405 through 408
      removed outlier: 6.224A  pdb=" N   ASP x 406 " --> pdb=" O   CYS x 561 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   ARG x 563 " --> pdb=" O   ASP x 406 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   HIS x 408 " --> pdb=" O   ARG x 563 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ASP x 437 " --> pdb=" O   ILE x 513 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE x 438 " --> pdb=" O   VAL x 498 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   ALA x 500 " --> pdb=" O   ILE x 438 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   VAL x 440 " --> pdb=" O   ALA x 500 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLN x 468 " --> pdb=" O   ARG x 495 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   VAL x 497 " --> pdb=" O   GLN x 468 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ILE x 470 " --> pdb=" O   VAL x 497 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU x 499 " --> pdb=" O   ILE x 470 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   THR x 472 " --> pdb=" O   LEU x 499 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'x' and resid 521 through 528
      removed outlier: 3.639A  pdb=" N   MET x 533 " --> pdb=" O   VAL x 528 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   THR x 534 " --> pdb=" O   LEU x 835 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   LEU x 837 " --> pdb=" O   THR x 534 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LEU x 536 " --> pdb=" O   LEU x 837 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'x' and resid 795 through 797
      removed outlier: 3.980A  pdb=" N   TYR x 829 " --> pdb=" O   ILE x 849 " (cutoff:3.500A)

    239 hydrogen bonds defined for protein.
    693 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: 1.87

  Time building geometry restraints manager: 1.61 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: 1869
        1.34 -     1.46: 828
        1.46 -     1.57: 3217
        1.57 -     1.69: 4
        1.69 -     1.81: 57
  Bond restraints: 5975
  Sorted by residual:
  bond pdb=" CA  ARG x 584 "
       pdb=" CB  ARG x 584 "
    ideal  model  delta    sigma   weight residual
    1.527  1.607 -0.080 2.48e-02 1.63e+03 1.04e+01
  bond pdb=" N   LEU x 375 "
       pdb=" CA  LEU x 375 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.21e-02 6.83e+03 6.56e+00
  bond pdb=" N   LEU x 374 "
       pdb=" CA  LEU x 374 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.21e-02 6.83e+03 6.26e+00
  bond pdb=" N   LYS x 373 "
       pdb=" CA  LYS x 373 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.21e-02 6.83e+03 5.99e+00
  bond pdb=" CA  THR y  93 "
       pdb=" CB  THR y  93 "
    ideal  model  delta    sigma   weight residual
    1.532  1.568 -0.035 2.01e-02 2.48e+03 3.11e+00
  ... (remaining 5970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 7749
        2.01 -     4.02: 269
        4.02 -     6.03: 33
        6.03 -     8.04: 17
        8.04 -    10.05: 7
  Bond angle restraints: 8075
  Sorted by residual:
  angle pdb=" C   THR x 838 "
        pdb=" N   SER x 839 "
        pdb=" CA  SER x 839 "
      ideal   model   delta    sigma   weight residual
     121.54  130.30   -8.76 1.91e+00 2.74e-01 2.10e+01
  angle pdb=" CA  ARG x 584 "
        pdb=" CB  ARG x 584 "
        pdb=" CG  ARG x 584 "
      ideal   model   delta    sigma   weight residual
     114.10  123.00   -8.90 2.00e+00 2.50e-01 1.98e+01
  angle pdb=" C   VAL y  92 "
        pdb=" N   THR y  93 "
        pdb=" CA  THR y  93 "
      ideal   model   delta    sigma   weight residual
     122.19  132.24  -10.05 2.30e+00 1.89e-01 1.91e+01
  angle pdb=" C   VAL x 174 "
        pdb=" N   PHE x 175 "
        pdb=" CA  PHE x 175 "
      ideal   model   delta    sigma   weight residual
     121.70  129.33   -7.63 1.80e+00 3.09e-01 1.80e+01
  angle pdb=" C   ASP x 601 "
        pdb=" N   LEU x 602 "
        pdb=" CA  LEU x 602 "
      ideal   model   delta    sigma   weight residual
     121.54  128.61   -7.07 1.91e+00 2.74e-01 1.37e+01
  ... (remaining 8070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.63: 3593
       28.63 -    57.25: 66
       57.25 -    85.88: 8
       85.88 -   114.51: 1
      114.51 -   143.14: 1
  Dihedral angle restraints: 3669
    sinusoidal: 1538
      harmonic: 2131
  Sorted by residual:
  dihedral pdb=" O1B ADP x1001 "
           pdb=" O3A ADP x1001 "
           pdb=" PB  ADP x1001 "
           pdb=" PA  ADP x1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  156.86  143.14     1      2.00e+01 2.50e-03 4.32e+01
  dihedral pdb=" O2A ADP x1001 "
           pdb=" O3A ADP x1001 "
           pdb=" PA  ADP x1001 "
           pdb=" PB  ADP x1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   33.71  -93.71     1      2.00e+01 2.50e-03 2.56e+01
  dihedral pdb=" CA  ALA y 161 "
           pdb=" C   ALA y 161 "
           pdb=" N   SER y 162 "
           pdb=" CA  SER y 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.60  -21.40     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 3666 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 582
       0.038 -    0.076: 220
       0.076 -    0.115: 80
       0.115 -    0.153: 44
       0.153 -    0.191: 5
  Chirality restraints: 931
  Sorted by residual:
  chirality pdb=" CB  ILE x 635 "
            pdb=" CA  ILE x 635 "
            pdb=" CG1 ILE x 635 "
            pdb=" CG2 ILE x 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CB  THR x 538 "
            pdb=" CA  THR x 538 "
            pdb=" OG1 THR x 538 "
            pdb=" CG2 THR x 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.77e-01
  chirality pdb=" CA  ILE x 767 "
            pdb=" N   ILE x 767 "
            pdb=" C   ILE x 767 "
            pdb=" CB  ILE x 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.97e-01
  ... (remaining 928 not shown)

  Planarity restraints: 1018
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET x 577 "    0.040 5.00e-02 4.00e+02   6.00e-02 5.75e+00
        pdb=" N   PRO x 578 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO x 578 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO x 578 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP x 518 "    0.036 5.00e-02 4.00e+02   5.43e-02 4.72e+00
        pdb=" N   PRO x 519 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO x 519 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO x 519 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS x 810 "   -0.035 5.00e-02 4.00e+02   5.24e-02 4.40e+00
        pdb=" N   PRO x 811 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO x 811 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO x 811 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1015 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 76
        2.65 -     3.21: 5022
        3.21 -     3.78: 8772
        3.78 -     4.34: 12538
        4.34 -     4.90: 20329
  Nonbonded interactions: 46737
  Sorted by model distance:
  nonbonded pdb=" O3B ADP x1001 "
            pdb="MG    MG x1002 "
     model   vdw
     2.092 2.170
  nonbonded pdb=" OG1 THR x 253 "
            pdb="MG    MG x1002 "
     model   vdw
     2.094 2.170
  nonbonded pdb=" O   GLN x 427 "
            pdb=" OG1 THR x 431 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   GLU x 581 "
            pdb=" OG1 THR x 585 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   SER x 530 "
            pdb=" OG  SER x 801 "
     model   vdw
     2.284 3.040
  ... (remaining 46732 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.760
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
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      :  0.005   0.080   5975  Z= 0.318
  Angle     :  0.917  10.046   8075  Z= 0.478
  Chirality :  0.052   0.191    931
  Planarity :  0.007   0.060   1018
  Dihedral  : 11.275 143.137   2287
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.51 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.88 (0.25), residues: 718
  helix: -3.17 (0.15), residues: 294
  sheet:  0.94 (0.49), residues: 106
  loop : -1.50 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP x 723 
 HIS   0.006   0.002   HIS x 704 
 PHE   0.023   0.002   PHE x 308 
 TYR   0.029   0.003   TYR x 321 
 ARG   0.004   0.001   ARG x 289 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.634 
Fit side-chains
REVERT: x  280 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7126 (ttm110)
REVERT: x  335 SER cc_start: 0.8158 (m) cc_final: 0.7907 (p)
REVERT: x  341 SER cc_start: 0.8794 (t) cc_final: 0.8257 (p)
REVERT: x  534 THR cc_start: 0.8690 (t) cc_final: 0.8428 (m)
REVERT: x  560 LYS cc_start: 0.8202 (mttt) cc_final: 0.7979 (mtpp)
REVERT: x  575 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7048 (mp0)
REVERT: x  632 LYS cc_start: 0.8573 (mptm) cc_final: 0.8299 (mmtt)
REVERT: x  770 TYR cc_start: 0.6622 (m-10) cc_final: 0.6395 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 171
  average time/residue: 0.2554
  time to fit residues: 52.8015
Evaluate side-chains
  95 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  374 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
x 255 GLN
x 258 GLN
x 382 ASN
x 408 HIS
x 419 HIS
x 427 GLN
x 429 HIS
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 548 GLN
x 663 GLN
x 834 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5975  Z= 0.268
  Angle     :  0.663   8.642   8075  Z= 0.336
  Chirality :  0.045   0.174    931
  Planarity :  0.006   0.041   1018
  Dihedral  :  8.134 137.062    801
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  9.60 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.66 (0.29), residues: 718
  helix: -0.49 (0.26), residues: 314
  sheet:  0.32 (0.45), residues: 107
  loop : -0.48 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP x 723 
 HIS   0.005   0.001   HIS x 704 
 PHE   0.020   0.002   PHE x 426 
 TYR   0.012   0.002   TYR x 171 
 ARG   0.004   0.001   ARG x 514 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.645 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8199 (m) cc_final: 0.7927 (p)
REVERT: x  357 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8395 (mm)
REVERT: x  632 LYS cc_start: 0.8647 (mptm) cc_final: 0.8414 (mmtm)
  outliers start: 14
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2087
  time to fit residues: 27.0157
Evaluate side-chains
  85 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  357 ILE
Chi-restraints excluded: chain x residue  374 LEU
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 65 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 445 GLN
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 622 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5975  Z= 0.198
  Angle     :  0.583   8.532   8075  Z= 0.293
  Chirality :  0.043   0.184    931
  Planarity :  0.004   0.041   1018
  Dihedral  :  7.260 124.384    801
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 10.82 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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 (0.30), residues: 718
  helix:  0.82 (0.28), residues: 312
  sheet:  0.50 (0.46), residues: 106
  loop : -0.50 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP y 115 
 HIS   0.003   0.001   HIS x 704 
 PHE   0.014   0.002   PHE x 426 
 TYR   0.013   0.001   TYR x 171 
 ARG   0.003   0.000   ARG x 514 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.633 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8113 (m) cc_final: 0.7855 (p)
REVERT: x  341 SER cc_start: 0.8772 (t) cc_final: 0.8245 (p)
REVERT: x  357 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8405 (mm)
REVERT: x  632 LYS cc_start: 0.8616 (mptm) cc_final: 0.8373 (mmtm)
  outliers start: 16
  outliers final: 13
  residues processed: 98
  average time/residue: 0.1914
  time to fit residues: 24.4457
Evaluate side-chains
  91 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  254 THR
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  357 ILE
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 727 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5975  Z= 0.298
  Angle     :  0.638   8.074   8075  Z= 0.319
  Chirality :  0.045   0.183    931
  Planarity :  0.005   0.037   1018
  Dihedral  :  6.938 105.772    799
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.35 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.60 (0.31), residues: 718
  helix:  1.15 (0.28), residues: 313
  sheet:  0.43 (0.43), residues: 126
  loop : -0.39 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP x 568 
 HIS   0.005   0.001   HIS x 704 
 PHE   0.023   0.002   PHE x 426 
 TYR   0.015   0.002   TYR x 171 
 ARG   0.003   0.001   ARG x 514 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.677 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8112 (m) cc_final: 0.7856 (p)
REVERT: x  341 SER cc_start: 0.8780 (t) cc_final: 0.8226 (p)
REVERT: x  357 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: x  575 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7064 (mp0)
REVERT: x  632 LYS cc_start: 0.8685 (mptm) cc_final: 0.8447 (mmtm)
  outliers start: 24
  outliers final: 20
  residues processed: 98
  average time/residue: 0.1846
  time to fit residues: 23.8273
Evaluate side-chains
  98 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  254 THR
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  357 ILE
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  508 LEU
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  545 SER
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  603 ILE
Chi-restraints excluded: chain x residue  686 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  762 MET
Chi-restraints excluded: chain x residue  836 MET
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 480 GLN
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   5975  Z= 0.457
  Angle     :  0.722   8.231   8075  Z= 0.362
  Chirality :  0.049   0.194    931
  Planarity :  0.006   0.058   1018
  Dihedral  :  7.176  99.560    799
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 13.57 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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 (0.31), residues: 718
  helix:  0.80 (0.28), residues: 318
  sheet:  0.14 (0.45), residues: 126
  loop : -0.38 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP x 568 
 HIS   0.006   0.001   HIS x 704 
 PHE   0.032   0.003   PHE x 426 
 TYR   0.016   0.002   TYR x 171 
 ARG   0.004   0.001   ARG x 543 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.714 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8117 (m) cc_final: 0.7851 (p)
REVERT: x  341 SER cc_start: 0.8803 (t) cc_final: 0.8259 (p)
REVERT: x  357 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8411 (mm)
REVERT: x  575 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7090 (mp0)
REVERT: x  632 LYS cc_start: 0.8728 (mptm) cc_final: 0.8471 (mmtm)
  outliers start: 24
  outliers final: 20
  residues processed: 95
  average time/residue: 0.1845
  time to fit residues: 23.0307
Evaluate side-chains
  99 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  245 MET
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  357 ILE
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  508 LEU
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  545 SER
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  603 ILE
Chi-restraints excluded: chain x residue  686 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  836 MET
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  862 ILE
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 480 GLN
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5975  Z= 0.179
  Angle     :  0.578   8.573   8075  Z= 0.289
  Chirality :  0.043   0.190    931
  Planarity :  0.004   0.033   1018
  Dihedral  :  6.755 100.514    799
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.09 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.68 (0.31), residues: 718
  helix:  1.40 (0.29), residues: 313
  sheet:  0.05 (0.45), residues: 129
  loop : -0.35 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 727 
 PHE   0.016   0.001   PHE x 426 
 TYR   0.011   0.001   TYR x 417 
 ARG   0.002   0.000   ARG x 514 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.568 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8003 (m) cc_final: 0.7784 (p)
REVERT: x  341 SER cc_start: 0.8762 (t) cc_final: 0.8253 (p)
REVERT: x  357 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8402 (mm)
REVERT: x  575 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7121 (mp0)
REVERT: x  632 LYS cc_start: 0.8686 (mptm) cc_final: 0.8433 (mmtm)
  outliers start: 18
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1811
  time to fit residues: 21.9076
Evaluate side-chains
  94 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  276 THR
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  357 ILE
Chi-restraints excluded: chain x residue  486 ILE
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  545 SER
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  686 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  862 ILE
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0030
   chunk 42 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.8192

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

Flipped N/Q/H residues before XYZ refinement:
x 239 ASN
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5975  Z= 0.175
  Angle     :  0.564   8.297   8075  Z= 0.280
  Chirality :  0.042   0.132    931
  Planarity :  0.004   0.031   1018
  Dihedral  :  6.540  96.801    799
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.94 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.88 (0.31), residues: 718
  helix:  1.64 (0.29), residues: 314
  sheet:  0.10 (0.47), residues: 128
  loop : -0.31 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 727 
 PHE   0.016   0.001   PHE x 426 
 TYR   0.011   0.001   TYR x 417 
 ARG   0.001   0.000   ARG x 369 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.736 
Fit side-chains
REVERT: x  357 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8397 (mm)
REVERT: x  575 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7121 (mp0)
REVERT: x  632 LYS cc_start: 0.8700 (mptm) cc_final: 0.8436 (mptt)
  outliers start: 21
  outliers final: 17
  residues processed: 91
  average time/residue: 0.1966
  time to fit residues: 23.6480
Evaluate side-chains
  92 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  276 THR
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  357 ILE
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  508 LEU
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  545 SER
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  762 MET
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  862 ILE
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0020
   chunk 47 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0040
   chunk 55 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0040
   overall best weight:    0.0610

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

Flipped N/Q/H residues before XYZ refinement:
x 277 GLN
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5975  Z= 0.113
  Angle     :  0.511   7.939   8075  Z= 0.252
  Chirality :  0.041   0.135    931
  Planarity :  0.004   0.028   1018
  Dihedral  :  5.950  84.285    799
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.77 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.24 (0.32), residues: 718
  helix:  1.97 (0.30), residues: 314
  sheet:  0.48 (0.48), residues: 123
  loop : -0.29 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP x 854 
 HIS   0.004   0.001   HIS x 727 
 PHE   0.008   0.001   PHE y 105 
 TYR   0.011   0.001   TYR x 304 
 ARG   0.002   0.000   ARG x 514 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.669 
Fit side-chains
REVERT: x  575 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7132 (mp0)
REVERT: x  798 MET cc_start: 0.7530 (mtp) cc_final: 0.7296 (mtp)
  outliers start: 13
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1920
  time to fit residues: 23.9030
Evaluate side-chains
  84 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  545 SER
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0070
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0170
   chunk 51 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5436

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 277 GLN
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5975  Z= 0.141
  Angle     :  0.524   8.175   8075  Z= 0.257
  Chirality :  0.041   0.128    931
  Planarity :  0.004   0.038   1018
  Dihedral  :  5.709  76.199    799
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.31 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.30 (0.32), residues: 718
  helix:  2.01 (0.30), residues: 315
  sheet:  0.61 (0.49), residues: 123
  loop : -0.30 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP x 568 
 HIS   0.003   0.001   HIS y 142 
 PHE   0.010   0.001   PHE x 426 
 TYR   0.010   0.001   TYR x 417 
 ARG   0.002   0.000   ARG x 514 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.767 
Fit side-chains
REVERT: x  385 LYS cc_start: 0.7830 (tttp) cc_final: 0.7526 (ttmt)
REVERT: x  575 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7121 (mp0)
  outliers start: 12
  outliers final: 10
  residues processed: 88
  average time/residue: 0.2213
  time to fit residues: 25.3683
Evaluate side-chains
  87 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  545 SER
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0000
   chunk 61 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0030
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5975  Z= 0.133
  Angle     :  0.523   8.150   8075  Z= 0.256
  Chirality :  0.041   0.129    931
  Planarity :  0.004   0.034   1018
  Dihedral  :  5.352  66.743    799
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.92 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.34 (0.32), residues: 718
  helix:  2.04 (0.30), residues: 315
  sheet:  0.53 (0.48), residues: 123
  loop : -0.22 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP x 568 
 HIS   0.003   0.001   HIS y 142 
 PHE   0.010   0.001   PHE x 426 
 TYR   0.010   0.001   TYR x 417 
 ARG   0.003   0.000   ARG x 307 

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.689 
Fit side-chains
REVERT: x  575 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7122 (mp0)
  outliers start: 11
  outliers final: 11
  residues processed: 84
  average time/residue: 0.1978
  time to fit residues: 21.7123
Evaluate side-chains
  87 residues out of total 657 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  469 MET
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  545 SER
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0370
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.133756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.106803 restraints weight = 6564.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.65
r_work: 0.2957 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5975  Z= 0.148
  Angle     :  0.534   8.125   8075  Z= 0.261
  Chirality :  0.041   0.130    931
  Planarity :  0.004   0.044   1018
  Dihedral  :  5.136  59.302    799
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.77 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.33 (0.32), residues: 718
  helix:  2.01 (0.30), residues: 315
  sheet:  0.51 (0.49), residues: 123
  loop : -0.19 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP x 568 
 HIS   0.003   0.001   HIS y 142 
 PHE   0.011   0.001   PHE x 426 
 TYR   0.010   0.001   TYR x 417 
 ARG   0.001   0.000   ARG x 514 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1720.83 seconds
wall clock time: 31 minutes 17.57 seconds (1877.57 seconds total)