Starting phenix.real_space_refine
on Sun Aug  4 04:36:39 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5x_44228/08_2024/9b5x_44228.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5x_44228/08_2024/9b5x_44228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5x_44228/08_2024/9b5x_44228.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5x_44228/08_2024/9b5x_44228.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5x_44228/08_2024/9b5x_44228.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5x_44228/08_2024/9b5x_44228.cif"
  }
  resolution = 4.16
  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=   0.034
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      42      5.16       5
     C    6074      2.51       5
     N    1573      2.21       5
     O    1833      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  237": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  250": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  295": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  360": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  384": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  421": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 9527
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.87, per 1000 atoms: 0.62
  Number of scatterers: 9527
  At special positions: 0
  Unit cell: (94.696, 97.888, 119.168, 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      42     16.00
     P       3     15.00
     Mg      2     11.99
     O    1833      8.00
     N    1573      7.00
     C    6074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.92

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.95
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 11 sheets defined
      46.1% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.825A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.686A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.958A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.221A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 3.705A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.220A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 304
      removed outlier: 3.950A  pdb=" N   GLN A 290 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.465A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.864A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG A 474 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
      removed outlier: 3.601A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.899A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 538 through 553
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
    Processing helix  chain 'A' and resid 618 through 628
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.511A  pdb=" N   LYS A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 3.528A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.766A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 736
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.928A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 4.112A  pdb=" N   GLN A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 794 " --> pdb=" O   ILE A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 834
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.532A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.530A  pdb=" N   LEU C  89 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 145
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 37 through 41
    Processing helix  chain 'D' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.637A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 7.089A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.599A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER A 460 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR A 462 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.258A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ASP A 996 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   VAL A 942 " --> pdb=" O   ASP A 996 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.258A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22
      removed outlier: 6.141A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22
    Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16
      removed outlier: 4.029A  pdb=" N   SER D  65 " --> pdb=" O   GLN D   2 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1269 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: 3.77

  Time building geometry restraints manager: 3.95 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1616
        1.27 -     1.40: 2291
        1.40 -     1.54: 5677
        1.54 -     1.67: 90
        1.67 -     1.81: 64
  Bond restraints: 9738
  Sorted by residual:
  bond pdb=" C04 A1AIV D 101 "
       pdb=" C05 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.526 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.71e+00
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.520  0.011 1.20e-02 6.94e+03 9.05e-01
  bond pdb=" C05 A1AIV D 101 "
       pdb=" N06 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 8.85e-01
  bond pdb=" C1' ATP A1103 "
       pdb=" O4' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.416  1.407  0.009 1.30e-02 5.92e+03 4.96e-01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
      100.18 -   115.93: 6456
      115.93 -   131.68: 6727
      131.68 -   147.43: 11
      147.43 -   163.18: 0
      163.18 -   178.93: 1
  Bond angle restraints: 13195
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  127.69   -5.99 1.80e+00 3.09e-01 1.11e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.47    3.06 1.18e+00 7.24e-01 6.80e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.99    4.20 1.76e+00 3.23e-01 5.69e+00
  angle pdb=" C4' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.06  105.26    5.80 2.50e+00 1.60e-01 5.39e+00
  angle pdb=" C1' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     110.58  104.61    5.97 2.79e+00 1.28e-01 4.57e+00
  ... (remaining 13190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.21: 5626
       15.21 -    30.42: 238
       30.42 -    45.63: 46
       45.63 -    60.84: 16
       60.84 -    76.05: 3
  Dihedral angle restraints: 5929
    sinusoidal: 2424
      harmonic: 3505
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.05   76.05     1      1.00e+01 1.00e-02 7.29e+01
  dihedral pdb=" CA  LYS A 884 "
           pdb=" C   LYS A 884 "
           pdb=" N   ASN A 885 "
           pdb=" CA  ASN A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.83   16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" N   GLU A 869 "
           pdb=" CA  GLU A 869 "
           pdb=" CB  GLU A 869 "
           pdb=" CG  GLU A 869 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.79   58.79     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 5926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1287
       0.055 -    0.111: 159
       0.111 -    0.166: 22
       0.166 -    0.221: 1
       0.221 -    0.276: 2
  Chirality restraints: 1471
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.90    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C4' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" C5' ATP A1103 "
            pdb=" O4' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.71    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1468 not shown)

  Planarity restraints: 1707
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 105 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   SER C 105 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER C 105 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE C 106 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 101 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.78e+00
        pdb=" C   LYS C 101 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LYS C 101 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL C 102 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 543 "    0.006 2.00e-02 2.50e+03   1.25e-02 1.55e+00
        pdb=" C   MET A 543 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   MET A 543 "    0.008 2.00e-02 2.50e+03
        pdb=" N   TYR A 544 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1704 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 97
        2.58 -     3.16: 8160
        3.16 -     3.74: 14407
        3.74 -     4.32: 20344
        4.32 -     4.90: 34294
  Nonbonded interactions: 77302
  Sorted by model distance:
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2A ATP A1103 "
     model   vdw
     2.006 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.027 2.170
  nonbonded pdb=" O   PRO C  18 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" OD1 ASP A 154 "
            pdb=" NH1 ARG A 156 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" OG  SER A 488 "
            pdb=" OE1 GLU A 489 "
     model   vdw
     2.184 3.040
  ... (remaining 77297 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.730
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     29.100
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
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      :  0.002   0.073   9738  Z= 0.133
  Angle     :  0.442   5.988  13195  Z= 0.228
  Chirality :  0.040   0.276   1471
  Planarity :  0.003   0.023   1707
  Dihedral  :  9.372  73.529   3662
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  2.83 %
    Favored  : 95.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  0.97 (0.25), residues: 1199
  helix:  1.52 (0.25), residues: 484
  sheet:  0.11 (0.35), residues: 208
  loop :  0.15 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  93 
 HIS   0.002   0.001   HIS D  68 
 PHE   0.008   0.001   PHE A 521 
 TYR   0.006   0.001   TYR A 277 
 ARG   0.002   0.000   ARG A 474 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9561 (ttp) cc_final: 0.9078 (tmm)
REVERT: A  158 LEU cc_start: 0.9603 (mt) cc_final: 0.9380 (mp)
REVERT: A  349 GLN cc_start: 0.8940 (mt0) cc_final: 0.8715 (pp30)
REVERT: A  413 GLN cc_start: 0.9359 (tt0) cc_final: 0.9116 (mt0)
REVERT: A  442 MET cc_start: 0.9785 (tpp) cc_final: 0.9224 (tpp)
REVERT: A  448 MET cc_start: 0.9193 (mmp) cc_final: 0.8493 (mmm)
REVERT: A  449 MET cc_start: 0.9468 (mtp) cc_final: 0.8874 (mmm)
REVERT: A  533 THR cc_start: 0.9247 (m) cc_final: 0.8611 (p)
REVERT: A  832 MET cc_start: 0.9308 (mtp) cc_final: 0.9008 (mtp)
REVERT: A  869 GLU cc_start: 0.9529 (OUTLIER) cc_final: 0.9288 (mm-30)
REVERT: A  941 GLU cc_start: 0.9373 (tt0) cc_final: 0.9049 (tm-30)
REVERT: C   74 TYR cc_start: 0.9130 (t80) cc_final: 0.8067 (t80)
REVERT: D    1 MET cc_start: 0.3807 (ptt) cc_final: 0.2537 (ptt)
REVERT: D   18 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8098 (mm-30)
  outliers start: 16
  outliers final: 6
  residues processed: 180
  average time/residue: 0.2547
  time to fit residues: 62.0420
Evaluate side-chains
  92 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0050
   chunk 93 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 69 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.3798

-------------------------------------------------------------------------------
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: 0.8330
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   9738  Z= 0.228
  Angle     :  0.543   6.102  13195  Z= 0.285
  Chirality :  0.042   0.165   1471
  Planarity :  0.004   0.064   1707
  Dihedral  :  5.206  56.390   1325
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.70 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.27 (0.25), residues: 1199
  helix:  1.51 (0.24), residues: 499
  sheet:  0.65 (0.39), residues: 194
  loop :  0.39 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  93 
 HIS   0.004   0.001   HIS C  55 
 PHE   0.010   0.001   PHE A 170 
 TYR   0.012   0.001   TYR A  81 
 ARG   0.014   0.001   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9647 (ttp) cc_final: 0.9136 (tmm)
REVERT: A   55 ASN cc_start: 0.9358 (m-40) cc_final: 0.8997 (m110)
REVERT: A  413 GLN cc_start: 0.9397 (tt0) cc_final: 0.9074 (mt0)
REVERT: A  442 MET cc_start: 0.9797 (tpp) cc_final: 0.9366 (tpp)
REVERT: A  448 MET cc_start: 0.9004 (mmp) cc_final: 0.8801 (mmm)
REVERT: A  449 MET cc_start: 0.9396 (mtp) cc_final: 0.8760 (mmm)
REVERT: A  464 MET cc_start: 0.9352 (pmm) cc_final: 0.8972 (pmm)
REVERT: A  855 MET cc_start: 0.9278 (tpt) cc_final: 0.8803 (tpp)
REVERT: C   30 LEU cc_start: 0.9671 (mm) cc_final: 0.9362 (mm)
REVERT: C   74 TYR cc_start: 0.9112 (t80) cc_final: 0.8566 (t80)
REVERT: D    1 MET cc_start: 0.4600 (ptt) cc_final: 0.3800 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2209
  time to fit residues: 34.1878
Evaluate side-chains
  67 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 116 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 107 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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: 0.8397
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9738  Z= 0.251
  Angle     :  0.548   6.032  13195  Z= 0.284
  Chirality :  0.041   0.129   1471
  Planarity :  0.004   0.048   1707
  Dihedral  :  5.287  58.783   1325
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.36 (0.25), residues: 1199
  helix:  1.56 (0.24), residues: 499
  sheet:  0.50 (0.41), residues: 193
  loop :  0.57 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  93 
 HIS   0.003   0.001   HIS A  29 
 PHE   0.014   0.001   PHE A 677 
 TYR   0.013   0.001   TYR C  60 
 ARG   0.006   0.001   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9682 (ttp) cc_final: 0.9135 (tmm)
REVERT: A   55 ASN cc_start: 0.9291 (m-40) cc_final: 0.8992 (m110)
REVERT: A  413 GLN cc_start: 0.9395 (tt0) cc_final: 0.8968 (mt0)
REVERT: A  442 MET cc_start: 0.9795 (tpp) cc_final: 0.9287 (tpp)
REVERT: A  464 MET cc_start: 0.9412 (pmm) cc_final: 0.9098 (pmm)
REVERT: A  533 THR cc_start: 0.9303 (m) cc_final: 0.8689 (p)
REVERT: A  543 MET cc_start: 0.9650 (mtt) cc_final: 0.9307 (ttt)
REVERT: A  832 MET cc_start: 0.9256 (mtm) cc_final: 0.8924 (ptm)
REVERT: A  855 MET cc_start: 0.9221 (tpt) cc_final: 0.8731 (tpp)
REVERT: A  869 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9346 (mm-30)
REVERT: C   30 LEU cc_start: 0.9751 (mm) cc_final: 0.9455 (mm)
REVERT: D    1 MET cc_start: 0.5480 (ptt) cc_final: 0.4691 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2027
  time to fit residues: 24.4260
Evaluate side-chains
  62 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0970
   chunk 11 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 108 optimal weight:    0.8980
   chunk 115 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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: 0.8366
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9738  Z= 0.162
  Angle     :  0.490   6.313  13195  Z= 0.254
  Chirality :  0.041   0.127   1471
  Planarity :  0.004   0.078   1707
  Dihedral  :  5.236  59.522   1325
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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 (0.25), residues: 1199
  helix:  1.60 (0.24), residues: 497
  sheet:  0.51 (0.40), residues: 193
  loop :  0.62 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 917 
 HIS   0.002   0.001   HIS A 292 
 PHE   0.026   0.001   PHE C  50 
 TYR   0.019   0.001   TYR C  74 
 ARG   0.010   0.000   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9692 (ttp) cc_final: 0.9190 (tmm)
REVERT: A   55 ASN cc_start: 0.9302 (m-40) cc_final: 0.8987 (m110)
REVERT: A  413 GLN cc_start: 0.9359 (tt0) cc_final: 0.8909 (mt0)
REVERT: A  442 MET cc_start: 0.9756 (tpp) cc_final: 0.9313 (tpp)
REVERT: A  448 MET cc_start: 0.9177 (mmp) cc_final: 0.8783 (mmm)
REVERT: A  449 MET cc_start: 0.9588 (mtp) cc_final: 0.8887 (mmt)
REVERT: A  464 MET cc_start: 0.9415 (pmm) cc_final: 0.9122 (pmm)
REVERT: A  533 THR cc_start: 0.9300 (m) cc_final: 0.8767 (p)
REVERT: A  543 MET cc_start: 0.9645 (mtt) cc_final: 0.9325 (ptm)
REVERT: A  832 MET cc_start: 0.9229 (mtm) cc_final: 0.8745 (ptp)
REVERT: A  855 MET cc_start: 0.9272 (tpt) cc_final: 0.8874 (tpp)
REVERT: A  869 GLU cc_start: 0.9524 (mm-30) cc_final: 0.9316 (mm-30)
REVERT: A  941 GLU cc_start: 0.9324 (tt0) cc_final: 0.8981 (tm-30)
REVERT: C   74 TYR cc_start: 0.9185 (t80) cc_final: 0.8427 (t80)
REVERT: D    1 MET cc_start: 0.5464 (ptt) cc_final: 0.4317 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.2012
  time to fit residues: 24.6922
Evaluate side-chains
  60 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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: 0.8376
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9738  Z= 0.155
  Angle     :  0.475   5.641  13195  Z= 0.244
  Chirality :  0.040   0.167   1471
  Planarity :  0.004   0.054   1707
  Dihedral  :  5.204  59.947   1325
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.51 (0.26), residues: 1199
  helix:  1.68 (0.24), residues: 498
  sheet:  0.53 (0.40), residues: 193
  loop :  0.67 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  93 
 HIS   0.003   0.001   HIS A  29 
 PHE   0.020   0.001   PHE C  50 
 TYR   0.014   0.001   TYR C  45 
 ARG   0.006   0.000   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9696 (ttp) cc_final: 0.9403 (ppp)
REVERT: A   55 ASN cc_start: 0.9305 (m-40) cc_final: 0.9013 (m110)
REVERT: A  286 MET cc_start: 0.9216 (pmm) cc_final: 0.8988 (pmm)
REVERT: A  413 GLN cc_start: 0.9421 (tt0) cc_final: 0.9051 (mt0)
REVERT: A  442 MET cc_start: 0.9736 (tpp) cc_final: 0.9321 (tpp)
REVERT: A  448 MET cc_start: 0.9094 (mmp) cc_final: 0.8844 (mmm)
REVERT: A  449 MET cc_start: 0.9568 (mtp) cc_final: 0.8723 (mmm)
REVERT: A  533 THR cc_start: 0.9237 (m) cc_final: 0.8493 (p)
REVERT: A  832 MET cc_start: 0.9224 (mtm) cc_final: 0.8765 (ptp)
REVERT: A  855 MET cc_start: 0.9281 (tpt) cc_final: 0.8884 (tpp)
REVERT: A  941 GLU cc_start: 0.9336 (tt0) cc_final: 0.8987 (tm-30)
REVERT: C   30 LEU cc_start: 0.9792 (mm) cc_final: 0.9573 (mm)
REVERT: C   74 TYR cc_start: 0.9185 (t80) cc_final: 0.8556 (t80)
REVERT: D    1 MET cc_start: 0.5521 (ptt) cc_final: 0.4746 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1949
  time to fit residues: 23.0041
Evaluate side-chains
  62 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 115 optimal weight:    7.9990
   chunk 95 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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: 0.8402
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9738  Z= 0.192
  Angle     :  0.493   5.665  13195  Z= 0.257
  Chirality :  0.040   0.171   1471
  Planarity :  0.004   0.058   1707
  Dihedral  :  5.207  59.908   1325
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.59 (0.26), residues: 1199
  helix:  1.78 (0.24), residues: 497
  sheet:  0.48 (0.40), residues: 193
  loop :  0.73 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  93 
 HIS   0.002   0.001   HIS C  75 
 PHE   0.016   0.001   PHE C  50 
 TYR   0.011   0.001   TYR C  60 
 ARG   0.009   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.147 
Fit side-chains
REVERT: A   35 MET cc_start: 0.9707 (ttp) cc_final: 0.9419 (ppp)
REVERT: A   55 ASN cc_start: 0.9292 (m-40) cc_final: 0.9015 (m110)
REVERT: A  286 MET cc_start: 0.9222 (pmm) cc_final: 0.8995 (pmm)
REVERT: A  413 GLN cc_start: 0.9413 (tt0) cc_final: 0.9040 (mt0)
REVERT: A  442 MET cc_start: 0.9732 (tpp) cc_final: 0.9323 (tpp)
REVERT: A  449 MET cc_start: 0.9572 (mtp) cc_final: 0.8720 (mmm)
REVERT: A  533 THR cc_start: 0.9261 (m) cc_final: 0.8548 (p)
REVERT: A  543 MET cc_start: 0.9592 (mmm) cc_final: 0.9373 (mmp)
REVERT: A  832 MET cc_start: 0.9259 (mtm) cc_final: 0.8833 (mtp)
REVERT: A  855 MET cc_start: 0.9297 (tpt) cc_final: 0.8892 (tpp)
REVERT: A  869 GLU cc_start: 0.9304 (mp0) cc_final: 0.9036 (mp0)
REVERT: A  941 GLU cc_start: 0.9356 (tt0) cc_final: 0.9014 (tm-30)
REVERT: C   74 TYR cc_start: 0.9227 (t80) cc_final: 0.8555 (t80)
REVERT: D    1 MET cc_start: 0.5295 (ptt) cc_final: 0.4697 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1990
  time to fit residues: 21.5809
Evaluate side-chains
  61 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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: 0.8395
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9738  Z= 0.160
  Angle     :  0.486   5.740  13195  Z= 0.250
  Chirality :  0.040   0.161   1471
  Planarity :  0.004   0.066   1707
  Dihedral  :  5.146  59.274   1325
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.64 (0.26), residues: 1199
  helix:  1.78 (0.24), residues: 498
  sheet:  0.55 (0.39), residues: 192
  loop :  0.77 (0.30), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  33 
 HIS   0.002   0.000   HIS A 292 
 PHE   0.020   0.001   PHE A 334 
 TYR   0.009   0.001   TYR C 134 
 ARG   0.010   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9613 (ttp) cc_final: 0.9403 (ppp)
REVERT: A   55 ASN cc_start: 0.9307 (m-40) cc_final: 0.9020 (m110)
REVERT: A  286 MET cc_start: 0.9208 (pmm) cc_final: 0.8970 (pmm)
REVERT: A  413 GLN cc_start: 0.9400 (tt0) cc_final: 0.9051 (mt0)
REVERT: A  442 MET cc_start: 0.9719 (tpp) cc_final: 0.9332 (tpp)
REVERT: A  448 MET cc_start: 0.9223 (mmp) cc_final: 0.8776 (mmm)
REVERT: A  449 MET cc_start: 0.9575 (mtp) cc_final: 0.8661 (mmm)
REVERT: A  533 THR cc_start: 0.9250 (m) cc_final: 0.8544 (p)
REVERT: A  543 MET cc_start: 0.9592 (mmm) cc_final: 0.9372 (mmp)
REVERT: A  832 MET cc_start: 0.9249 (mtm) cc_final: 0.8827 (mtp)
REVERT: A  855 MET cc_start: 0.9280 (tpt) cc_final: 0.8881 (tpp)
REVERT: A  869 GLU cc_start: 0.9235 (mp0) cc_final: 0.8792 (mp0)
REVERT: A  941 GLU cc_start: 0.9357 (tt0) cc_final: 0.9016 (tm-30)
REVERT: C   74 TYR cc_start: 0.9200 (t80) cc_final: 0.8533 (t80)
REVERT: C  101 LYS cc_start: 0.9581 (pttm) cc_final: 0.9329 (tptt)
REVERT: D    1 MET cc_start: 0.5625 (ptt) cc_final: 0.4465 (ptt)
REVERT: D   18 GLU cc_start: 0.7915 (pp20) cc_final: 0.7643 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2029
  time to fit residues: 22.5131
Evaluate side-chains
  62 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    0.4980
   chunk 34 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0970
   chunk 72 optimal weight:    0.0980
   chunk 78 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 104 optimal weight:    0.4980
   chunk 109 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.2436

-------------------------------------------------------------------------------
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: 0.8367
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9738  Z= 0.129
  Angle     :  0.474   5.571  13195  Z= 0.244
  Chirality :  0.041   0.157   1471
  Planarity :  0.003   0.044   1707
  Dihedral  :  5.111  59.182   1325
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.65 (0.26), residues: 1199
  helix:  1.77 (0.25), residues: 498
  sheet:  0.57 (0.40), residues: 192
  loop :  0.81 (0.30), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  93 
 HIS   0.003   0.000   HIS A 292 
 PHE   0.026   0.001   PHE A  82 
 TYR   0.009   0.001   TYR C  74 
 ARG   0.003   0.000   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9674 (ttp) cc_final: 0.9419 (ppp)
REVERT: A   55 ASN cc_start: 0.9312 (m-40) cc_final: 0.9014 (m110)
REVERT: A  413 GLN cc_start: 0.9340 (tt0) cc_final: 0.9127 (mt0)
REVERT: A  442 MET cc_start: 0.9686 (tpp) cc_final: 0.9336 (tpp)
REVERT: A  448 MET cc_start: 0.9204 (mmp) cc_final: 0.8956 (mmm)
REVERT: A  449 MET cc_start: 0.9553 (mtp) cc_final: 0.9171 (mtt)
REVERT: A  533 THR cc_start: 0.9176 (m) cc_final: 0.8463 (p)
REVERT: A  832 MET cc_start: 0.9223 (mtm) cc_final: 0.8875 (ptm)
REVERT: A  855 MET cc_start: 0.9278 (tpt) cc_final: 0.8855 (tpp)
REVERT: A  865 LEU cc_start: 0.9673 (mt) cc_final: 0.9443 (mt)
REVERT: A  869 GLU cc_start: 0.9214 (mp0) cc_final: 0.8754 (mp0)
REVERT: A  941 GLU cc_start: 0.9356 (tt0) cc_final: 0.9004 (tm-30)
REVERT: C   74 TYR cc_start: 0.9203 (t80) cc_final: 0.8558 (t80)
REVERT: C  126 VAL cc_start: 0.9607 (t) cc_final: 0.9298 (p)
REVERT: D    1 MET cc_start: 0.5347 (ptt) cc_final: 0.4338 (ptt)
REVERT: D   18 GLU cc_start: 0.7763 (pp20) cc_final: 0.7375 (pp20)
REVERT: D   19 SER cc_start: 0.7110 (m) cc_final: 0.6665 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.2010
  time to fit residues: 23.5935
Evaluate side-chains
  65 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 109 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 96 optimal weight:    8.9990
   chunk 101 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 68 optimal weight:    0.2980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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: 0.8382
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9738  Z= 0.149
  Angle     :  0.478   5.445  13195  Z= 0.245
  Chirality :  0.040   0.155   1471
  Planarity :  0.003   0.041   1707
  Dihedral  :  5.090  59.731   1325
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.62 (0.26), residues: 1199
  helix:  1.73 (0.24), residues: 498
  sheet:  0.55 (0.38), residues: 204
  loop :  0.82 (0.30), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  33 
 HIS   0.002   0.000   HIS A 819 
 PHE   0.025   0.001   PHE A  82 
 TYR   0.011   0.001   TYR A 579 
 ARG   0.005   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A   35 MET cc_start: 0.9667 (ttp) cc_final: 0.9424 (ppp)
REVERT: A   55 ASN cc_start: 0.9300 (m-40) cc_final: 0.9009 (m110)
REVERT: A  442 MET cc_start: 0.9691 (tpp) cc_final: 0.9316 (tpp)
REVERT: A  448 MET cc_start: 0.9209 (mmp) cc_final: 0.8987 (mmm)
REVERT: A  449 MET cc_start: 0.9559 (mtp) cc_final: 0.9172 (mtt)
REVERT: A  533 THR cc_start: 0.9197 (m) cc_final: 0.8532 (p)
REVERT: A  832 MET cc_start: 0.9247 (mtm) cc_final: 0.8816 (ptp)
REVERT: A  855 MET cc_start: 0.9253 (tpt) cc_final: 0.8837 (tpp)
REVERT: A  941 GLU cc_start: 0.9357 (tt0) cc_final: 0.9005 (tm-30)
REVERT: C   74 TYR cc_start: 0.9194 (t80) cc_final: 0.8488 (t80)
REVERT: C  101 LYS cc_start: 0.9482 (pttm) cc_final: 0.9267 (tptt)
REVERT: C  126 VAL cc_start: 0.9622 (t) cc_final: 0.9338 (p)
REVERT: D    1 MET cc_start: 0.5501 (ptt) cc_final: 0.4400 (ptt)
REVERT: D   18 GLU cc_start: 0.7779 (pp20) cc_final: 0.7389 (pp20)
REVERT: D   19 SER cc_start: 0.7121 (m) cc_final: 0.6644 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2116
  time to fit residues: 24.3371
Evaluate side-chains
  62 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 118 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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: 0.8426
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9738  Z= 0.198
  Angle     :  0.511   5.832  13195  Z= 0.264
  Chirality :  0.040   0.153   1471
  Planarity :  0.003   0.042   1707
  Dihedral  :  5.146  59.618   1325
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.69 (0.26), residues: 1199
  helix:  1.82 (0.24), residues: 498
  sheet:  0.48 (0.39), residues: 191
  loop :  0.84 (0.30), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 917 
 HIS   0.003   0.001   HIS C  75 
 PHE   0.019   0.001   PHE A  82 
 TYR   0.013   0.001   TYR C  60 
 ARG   0.004   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.231 
Fit side-chains
REVERT: A   35 MET cc_start: 0.9673 (ttp) cc_final: 0.9429 (ppp)
REVERT: A  442 MET cc_start: 0.9739 (tpp) cc_final: 0.9319 (tpp)
REVERT: A  448 MET cc_start: 0.9336 (mmp) cc_final: 0.9024 (mmm)
REVERT: A  449 MET cc_start: 0.9460 (mtp) cc_final: 0.9229 (mtt)
REVERT: A  533 THR cc_start: 0.9245 (m) cc_final: 0.8586 (p)
REVERT: A  832 MET cc_start: 0.9284 (mtm) cc_final: 0.8862 (mtp)
REVERT: A  855 MET cc_start: 0.9301 (tpt) cc_final: 0.8885 (tpp)
REVERT: A  869 GLU cc_start: 0.9465 (mp0) cc_final: 0.9071 (mp0)
REVERT: A  941 GLU cc_start: 0.9360 (tt0) cc_final: 0.9020 (tm-30)
REVERT: C   74 TYR cc_start: 0.9265 (t80) cc_final: 0.8541 (t80)
REVERT: D    1 MET cc_start: 0.5342 (ptt) cc_final: 0.4137 (ptt)
REVERT: D   18 GLU cc_start: 0.7922 (pp20) cc_final: 0.7537 (pp20)
REVERT: D   19 SER cc_start: 0.7307 (m) cc_final: 0.6787 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1981
  time to fit residues: 21.4456
Evaluate side-chains
  59 residues out of total 1061 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0270
   chunk 39 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 83 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 68 optimal weight:    0.0970
   overall best weight:    0.5238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.035011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.026930 restraints weight = 85171.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.027790 restraints weight = 58166.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.028433 restraints weight = 43815.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9738  Z= 0.144
  Angle     :  0.491  10.193  13195  Z= 0.252
  Chirality :  0.041   0.155   1471
  Planarity :  0.003   0.042   1707
  Dihedral  :  5.111  58.674   1325
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.66 (0.26), residues: 1199
  helix:  1.76 (0.24), residues: 497
  sheet:  0.46 (0.39), residues: 192
  loop :  0.88 (0.30), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 702 
 HIS   0.003   0.000   HIS A 292 
 PHE   0.021   0.001   PHE A  82 
 TYR   0.010   0.001   TYR C  60 
 ARG   0.002   0.000   ARG A 671 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 1910.79 seconds
wall clock time: 34 minutes 54.47 seconds (2094.47 seconds total)