Starting phenix.real_space_refine
on Sun Mar 10 21:11:22 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/03_2024/8u1d_41810.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/03_2024/8u1d_41810.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/03_2024/8u1d_41810.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/03_2024/8u1d_41810.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/03_2024/8u1d_41810.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/03_2024/8u1d_41810.pdb"
  }
  resolution = 4.25
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    3195      2.51       5
     N     882      2.21       5
     O     997      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   57": "OD1" <-> "OD2"
    Residue "A PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  233": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  275": "OE1" <-> "OE2"
    Residue "A TYR  330": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  368": "OD1" <-> "OD2"
    Residue "A TYR  384": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  435": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I GLU    5": "OE1" <-> "OE2"
    Residue "I TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I GLU   61": "OE1" <-> "OE2"
    Residue "I TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 5109
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3310
          Classifications: {'peptide': 421}
          Link IDs: {'PTRANS': 18, 'TRANS': 402}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 969
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "J"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.27, per 1000 atoms: 0.64
  Number of scatterers: 5109
  At special positions: 0
  Unit cell: (89.64, 84.24, 85.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O     997      8.00
     N     882      7.00
     C    3195      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS A 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 239 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 296 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 378 " - pdb=" SG  CYS A 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 385 " - pdb=" SG  CYS A 418 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  23 " - pdb=" SG  CYS J  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 386 "
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 910.2 milliseconds
  

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 14 sheets defined
      13.8% alpha, 35.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 70
    Processing helix  chain 'A' and resid 71 through 73
      No H-bonds generated for 'chain 'A' and resid 71 through 73'
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 4.125A  pdb=" N   GLN A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 126
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 3.644A  pdb=" N   ILE A 141 " --> pdb=" O   ASN A 138 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE A 142 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 138 through 142'
    Processing helix  chain 'A' and resid 205 through 209
      removed outlier: 3.518A  pdb=" N   VAL A 208 " --> pdb=" O   CYS A 205 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER A 209 " --> pdb=" O   PRO A 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 205 through 209'
    Processing helix  chain 'A' and resid 334 through 350
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 3.826A  pdb=" N   THR A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
      removed outlier: 3.571A  pdb=" N   PHE A 391 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ASN A 392 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 388 through 392'
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'I' and resid 28 through 32
      removed outlier: 4.220A  pdb=" N   TYR I  32 " --> pdb=" O   PHE I  29 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 83 through 87
      removed outlier: 3.967A  pdb=" N   THR I  87 " --> pdb=" O   SER I  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86
      removed outlier: 3.637A  pdb=" N   SER A 243 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL A 245 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ILE A 225 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 224 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 94
    Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174
    Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203
      removed outlier: 6.377A  pdb=" N   VAL A 200 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   TYR A 435 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   THR A 202 " --> pdb=" O   TYR A 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261
      removed outlier: 6.556A  pdb=" N   LEU A 260 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
      removed outlier: 11.117A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261
      removed outlier: 6.556A  pdb=" N   LEU A 260 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
      removed outlier: 11.117A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU A 295 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE A 382 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 307
      removed outlier: 6.898A  pdb=" N   ASN A 301 " --> pdb=" O   VAL A 322 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   VAL A 322 " --> pdb=" O   ASN A 301 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   THR A 303 " --> pdb=" O   GLY A 321 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 361
      removed outlier: 6.928A  pdb=" N   ASN A 357 " --> pdb=" O   GLU A 464 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   PHE A 466 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR A 359 " --> pdb=" O   PHE A 466 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 3 through 6
      removed outlier: 3.527A  pdb=" N   LEU I  82 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 57 through 58
      removed outlier: 6.056A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER I 102 " --> pdb=" O   ARG I  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 57 through 58
      removed outlier: 6.056A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 5 through 6
      removed outlier: 3.800A  pdb=" N   ASP J  70 " --> pdb=" O   SER J  67 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER J  67 " --> pdb=" O   ASP J  70 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 10 through 13
      removed outlier: 6.064A  pdb=" N   LEU J  11 " --> pdb=" O   ASP J 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'J' and resid 53 through 54
      removed outlier: 6.542A  pdb=" N   ALA J  46 " --> pdb=" O   GLN J  37 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   GLN J  37 " --> pdb=" O   ALA J  46 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ILE J  48 " --> pdb=" O   TRP J  35 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    420 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: 1.57

  Time building geometry restraints manager: 1.92 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: 1654
        1.34 -     1.46: 1222
        1.46 -     1.59: 2297
        1.59 -     1.71: 0
        1.71 -     1.83: 48
  Bond restraints: 5221
  Sorted by residual:
  bond pdb=" N   ASP A  78 "
       pdb=" CA  ASP A  78 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.027 7.10e-03 1.98e+04 1.46e+01
  bond pdb=" N   ILE A 271 "
       pdb=" CA  ILE A 271 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.11e-02 8.12e+03 1.02e+01
  bond pdb=" N   VAL A 281 "
       pdb=" CA  VAL A 281 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.19e-02 7.06e+03 1.00e+01
  bond pdb=" N   VAL A  65 "
       pdb=" CA  VAL A  65 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.12e+00
  bond pdb=" N   VAL A 286 "
       pdb=" CA  VAL A 286 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.24e-02 6.50e+03 8.07e+00
  ... (remaining 5216 not shown)

  Histogram of bond angle deviations from ideal:
       99.20 -   106.21: 126
      106.21 -   113.21: 2773
      113.21 -   120.21: 1860
      120.21 -   127.21: 2260
      127.21 -   134.21: 66
  Bond angle restraints: 7085
  Sorted by residual:
  angle pdb=" N   LYS A  63 "
        pdb=" CA  LYS A  63 "
        pdb=" C   LYS A  63 "
      ideal   model   delta    sigma   weight residual
     113.28  107.17    6.11 1.22e+00 6.72e-01 2.50e+01
  angle pdb=" N   ILE J  29 "
        pdb=" CA  ILE J  29 "
        pdb=" C   ILE J  29 "
      ideal   model   delta    sigma   weight residual
     112.17  107.96    4.21 9.50e-01 1.11e+00 1.96e+01
  angle pdb=" N   VAL A  68 "
        pdb=" CA  VAL A  68 "
        pdb=" C   VAL A  68 "
      ideal   model   delta    sigma   weight residual
     113.16  106.66    6.50 1.49e+00 4.50e-01 1.90e+01
  angle pdb=" C   PRO I  41 "
        pdb=" N   ARG I  42 "
        pdb=" CA  ARG I  42 "
      ideal   model   delta    sigma   weight residual
     121.54  129.09   -7.55 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" CB  GLN I  39 "
        pdb=" CG  GLN I  39 "
        pdb=" CD  GLN I  39 "
      ideal   model   delta    sigma   weight residual
     112.60  119.26   -6.66 1.70e+00 3.46e-01 1.54e+01
  ... (remaining 7080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 2836
       17.29 -    34.58: 248
       34.58 -    51.87: 59
       51.87 -    69.16: 6
       69.16 -    86.46: 4
  Dihedral angle restraints: 3153
    sinusoidal: 1264
      harmonic: 1889
  Sorted by residual:
  dihedral pdb=" CA  GLU A 429 "
           pdb=" C   GLU A 429 "
           pdb=" N   VAL A 430 "
           pdb=" CA  VAL A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.51   22.49     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CB  CYS J  23 "
           pdb=" SG  CYS J  23 "
           pdb=" SG  CYS J  88 "
           pdb=" CB  CYS J  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.77  -37.77     1      1.00e+01 1.00e-02 2.01e+01
  dihedral pdb=" CA  MET A 434 "
           pdb=" C   MET A 434 "
           pdb=" N   TYR A 435 "
           pdb=" CA  TYR A 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.78   22.22     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 3150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 617
       0.071 -    0.143: 138
       0.143 -    0.214: 30
       0.214 -    0.285: 3
       0.285 -    0.357: 1
  Chirality restraints: 789
  Sorted by residual:
  chirality pdb=" CB  VAL A 208 "
            pdb=" CA  VAL A 208 "
            pdb=" CG1 VAL A 208 "
            pdb=" CG2 VAL A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CB  ILE A 326 "
            pdb=" CA  ILE A 326 "
            pdb=" CG1 ILE A 326 "
            pdb=" CG2 ILE A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  GLU J  81 "
            pdb=" N   GLU J  81 "
            pdb=" C   GLU J  81 "
            pdb=" CB  GLU J  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 786 not shown)

  Planarity restraints: 910
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER J  94 "   -0.047 5.00e-02 4.00e+02   7.11e-02 8.09e+00
        pdb=" N   PRO J  95 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO J  95 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO J  95 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP I 103 "   -0.015 2.00e-02 2.50e+03   1.54e-02 5.92e+00
        pdb=" CG  TRP I 103 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP I 103 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP I 103 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP I 103 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP I 103 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP I 103 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP I 103 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP I 103 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP I 103 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN J  79 "    0.037 5.00e-02 4.00e+02   5.55e-02 4.92e+00
        pdb=" N   PRO J  80 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO J  80 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO J  80 "    0.031 5.00e-02 4.00e+02
  ... (remaining 907 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1334
        2.80 -     3.33: 4531
        3.33 -     3.85: 8162
        3.85 -     4.38: 8702
        4.38 -     4.90: 15210
  Nonbonded interactions: 37939
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 103 "
            pdb=" OD2 ASP A 107 "
     model   vdw
     2.280 2.520
  nonbonded pdb=" OG  SER J  14 "
            pdb=" OD2 ASP J  17 "
     model   vdw
     2.304 2.440
  nonbonded pdb=" OG  SER A 479 "
            pdb=" OE1 GLU A 480 "
     model   vdw
     2.334 2.440
  nonbonded pdb=" O   PHE I 100E"
            pdb=" OH  TYR J  36 "
     model   vdw
     2.334 2.440
  nonbonded pdb=" O   GLN J   3 "
            pdb=" OG  SER J  26 "
     model   vdw
     2.347 2.440
  ... (remaining 37934 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.350
  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:          6.870
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     18.120
  Find NCS groups from input model:        0.140
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
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      :  0.006   0.056   5221  Z= 0.393
  Angle     :  1.055   9.252   7085  Z= 0.610
  Chirality :  0.064   0.357    789
  Planarity :  0.007   0.071    909
  Dihedral  : 13.613  86.455   1917
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.94 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  1.22 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.30), residues: 642
  helix: -2.35 (0.52), residues: 57
  sheet: -0.76 (0.36), residues: 189
  loop : -1.87 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP I 103 
 HIS   0.016   0.002   HIS I  35 
 PHE   0.012   0.002   PHE A 210 
 TYR   0.033   0.003   TYR A 330 
 ARG   0.014   0.001   ARG J  42 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8241 (p) cc_final: 0.7914 (t)
REVERT: A  396 MET cc_start: 0.6848 (ppp) cc_final: 0.6360 (ppp)
REVERT: I    3 HIS cc_start: 0.8035 (t-90) cc_final: 0.7531 (t-90)
REVERT: I   12 LYS cc_start: 0.8432 (mptt) cc_final: 0.8214 (mmtt)
REVERT: I   80 MET cc_start: 0.8926 (ttt) cc_final: 0.8424 (ttp)
REVERT: J    2 ILE cc_start: 0.7936 (mp) cc_final: 0.7267 (mp)
REVERT: J    4 MET cc_start: 0.7089 (mpp) cc_final: 0.6819 (mpp)
REVERT: J   58 VAL cc_start: 0.8674 (t) cc_final: 0.8212 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 139
  average time/residue: 0.1612
  time to fit residues: 28.9817
Evaluate side-chains
  97 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0050
   chunk 58 optimal weight:    0.0270
   overall best weight:    0.4652

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
A 258 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5221  Z= 0.168
  Angle     :  0.566   6.109   7085  Z= 0.305
  Chirality :  0.042   0.139    789
  Planarity :  0.004   0.054    909
  Dihedral  :  5.806  40.579    725
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.76 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.31), residues: 642
  helix: -0.69 (0.67), residues: 52
  sheet: -0.48 (0.39), residues: 166
  loop : -1.48 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP I  50 
 HIS   0.004   0.001   HIS I  35 
 PHE   0.015   0.001   PHE A 233 
 TYR   0.014   0.001   TYR A 330 
 ARG   0.005   0.000   ARG J  42 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8571 (p) cc_final: 0.8277 (t)
REVERT: A  122 LEU cc_start: 0.9201 (tp) cc_final: 0.8981 (tp)
REVERT: A  396 MET cc_start: 0.6885 (ppp) cc_final: 0.6355 (ppp)
REVERT: I    3 HIS cc_start: 0.8012 (t-90) cc_final: 0.7758 (t-90)
REVERT: I   80 MET cc_start: 0.8914 (ttt) cc_final: 0.8402 (ttp)
REVERT: J    2 ILE cc_start: 0.7911 (mp) cc_final: 0.7350 (mp)
REVERT: J   79 GLN cc_start: 0.8123 (pp30) cc_final: 0.7765 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1556
  time to fit residues: 24.8108
Evaluate side-chains
  90 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5221  Z= 0.224
  Angle     :  0.581   5.120   7085  Z= 0.310
  Chirality :  0.042   0.144    789
  Planarity :  0.004   0.047    909
  Dihedral  :  5.489  24.173    725
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.01 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.32), residues: 642
  helix: -0.26 (0.69), residues: 53
  sheet: -0.23 (0.39), residues: 179
  loop : -1.42 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP I  50 
 HIS   0.003   0.001   HIS A 216 
 PHE   0.015   0.002   PHE A 233 
 TYR   0.018   0.002   TYR I  32 
 ARG   0.005   0.001   ARG J  42 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8552 (p) cc_final: 0.8242 (t)
REVERT: A  122 LEU cc_start: 0.9241 (tp) cc_final: 0.8981 (tp)
REVERT: A  269 GLU cc_start: 0.7042 (pm20) cc_final: 0.6808 (tp30)
REVERT: A  396 MET cc_start: 0.6962 (ppp) cc_final: 0.6329 (ppp)
REVERT: I    3 HIS cc_start: 0.8033 (t-90) cc_final: 0.7812 (t-90)
REVERT: I    4 LEU cc_start: 0.8190 (mt) cc_final: 0.7858 (mt)
REVERT: I   71 ARG cc_start: 0.9046 (ppt170) cc_final: 0.8326 (ptt90)
REVERT: I   80 MET cc_start: 0.8842 (ttt) cc_final: 0.8480 (ttp)
REVERT: J    2 ILE cc_start: 0.8128 (mp) cc_final: 0.7685 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1605
  time to fit residues: 24.4436
Evaluate side-chains
  89 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0670
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   5221  Z= 0.168
  Angle     :  0.557   5.689   7085  Z= 0.296
  Chirality :  0.042   0.159    789
  Planarity :  0.004   0.046    909
  Dihedral  :  5.279  22.673    725
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.92 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.33), residues: 642
  helix:  0.81 (0.77), residues: 47
  sheet: -0.16 (0.39), residues: 186
  loop : -1.36 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I  50 
 HIS   0.006   0.001   HIS J  90 
 PHE   0.037   0.002   PHE J  83 
 TYR   0.011   0.001   TYR A 330 
 ARG   0.005   0.000   ARG J  42 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8571 (p) cc_final: 0.8270 (t)
REVERT: A  236 THR cc_start: 0.8128 (m) cc_final: 0.7887 (m)
REVERT: A  269 GLU cc_start: 0.7137 (pm20) cc_final: 0.6749 (tp30)
REVERT: A  396 MET cc_start: 0.6965 (ppp) cc_final: 0.6365 (ppp)
REVERT: A  434 MET cc_start: 0.8066 (ttm) cc_final: 0.7653 (tpp)
REVERT: I    4 LEU cc_start: 0.8203 (mt) cc_final: 0.7922 (mt)
REVERT: I   80 MET cc_start: 0.8944 (ttt) cc_final: 0.8367 (ttp)
REVERT: J   79 GLN cc_start: 0.8044 (pp30) cc_final: 0.7577 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1541
  time to fit residues: 23.6020
Evaluate side-chains
  90 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0770
   chunk 31 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5221  Z= 0.193
  Angle     :  0.588  12.321   7085  Z= 0.304
  Chirality :  0.042   0.163    789
  Planarity :  0.004   0.046    909
  Dihedral  :  5.261  21.388    725
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.54 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.32), residues: 642
  helix:  0.33 (0.72), residues: 53
  sheet: -0.14 (0.38), residues: 179
  loop : -1.36 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I  50 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.013   0.001   PHE A 233 
 TYR   0.012   0.001   TYR J  91 
 ARG   0.005   0.001   ARG J  42 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8538 (p) cc_final: 0.8249 (t)
REVERT: A  236 THR cc_start: 0.8141 (m) cc_final: 0.7866 (m)
REVERT: A  347 LYS cc_start: 0.8479 (pttt) cc_final: 0.8216 (tptp)
REVERT: A  396 MET cc_start: 0.6936 (ppp) cc_final: 0.6407 (ppp)
REVERT: A  426 MET cc_start: 0.6501 (tmm) cc_final: 0.6043 (tmm)
REVERT: A  434 MET cc_start: 0.7994 (ttm) cc_final: 0.7510 (tpp)
REVERT: I    4 LEU cc_start: 0.8209 (mt) cc_final: 0.7951 (mt)
REVERT: I   71 ARG cc_start: 0.8646 (ptt90) cc_final: 0.7995 (ptt90)
REVERT: I   80 MET cc_start: 0.8952 (ttt) cc_final: 0.8311 (ttp)
REVERT: J   79 GLN cc_start: 0.8312 (pp30) cc_final: 0.7950 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1506
  time to fit residues: 23.4998
Evaluate side-chains
  90 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5221  Z= 0.188
  Angle     :  0.574   5.639   7085  Z= 0.304
  Chirality :  0.042   0.158    789
  Planarity :  0.004   0.051    909
  Dihedral  :  5.217  21.056    725
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.07 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.32), residues: 642
  helix:  0.78 (0.74), residues: 47
  sheet: -0.17 (0.38), residues: 181
  loop : -1.44 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I  50 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.021   0.001   PHE J  83 
 TYR   0.023   0.002   TYR J  87 
 ARG   0.006   0.001   ARG J  42 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8475 (p) cc_final: 0.8165 (t)
REVERT: A  236 THR cc_start: 0.8136 (m) cc_final: 0.7839 (m)
REVERT: A  347 LYS cc_start: 0.8470 (pttt) cc_final: 0.8211 (tptp)
REVERT: A  396 MET cc_start: 0.6926 (ppp) cc_final: 0.6400 (ppp)
REVERT: A  434 MET cc_start: 0.7991 (ttm) cc_final: 0.7576 (tpp)
REVERT: I    3 HIS cc_start: 0.8011 (t-90) cc_final: 0.7575 (t-90)
REVERT: I    4 LEU cc_start: 0.8236 (mt) cc_final: 0.7862 (mt)
REVERT: I   71 ARG cc_start: 0.8503 (ptt90) cc_final: 0.7763 (ptt90)
REVERT: I   80 MET cc_start: 0.8893 (ttt) cc_final: 0.8321 (ttp)
REVERT: J    2 ILE cc_start: 0.8114 (mp) cc_final: 0.7913 (mt)
REVERT: J   79 GLN cc_start: 0.8275 (pp30) cc_final: 0.7684 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1599
  time to fit residues: 24.1555
Evaluate side-chains
  88 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5221  Z= 0.257
  Angle     :  0.624  11.627   7085  Z= 0.322
  Chirality :  0.042   0.143    789
  Planarity :  0.004   0.049    909
  Dihedral  :  5.405  20.178    725
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.10 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.32), residues: 642
  helix:  0.14 (0.71), residues: 53
  sheet: -0.25 (0.37), residues: 196
  loop : -1.42 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP I  50 
 HIS   0.004   0.001   HIS I  35 
 PHE   0.010   0.002   PHE A 233 
 TYR   0.015   0.002   TYR I  91 
 ARG   0.006   0.001   ARG J  42 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8537 (p) cc_final: 0.8233 (t)
REVERT: A  236 THR cc_start: 0.8238 (m) cc_final: 0.8001 (m)
REVERT: A  347 LYS cc_start: 0.8482 (pttt) cc_final: 0.8218 (tptp)
REVERT: A  396 MET cc_start: 0.7054 (ppp) cc_final: 0.6538 (ppp)
REVERT: A  426 MET cc_start: 0.6668 (tmm) cc_final: 0.6203 (tmm)
REVERT: A  434 MET cc_start: 0.8025 (ttm) cc_final: 0.7473 (tpp)
REVERT: I    3 HIS cc_start: 0.8128 (t-90) cc_final: 0.7622 (t-90)
REVERT: I    4 LEU cc_start: 0.8162 (mt) cc_final: 0.7751 (mt)
REVERT: I   47 TRP cc_start: 0.7650 (t-100) cc_final: 0.7016 (t-100)
REVERT: I   71 ARG cc_start: 0.8593 (ptt90) cc_final: 0.7855 (ptt90)
REVERT: I   80 MET cc_start: 0.8940 (ttt) cc_final: 0.8290 (ttp)
REVERT: J   79 GLN cc_start: 0.8321 (pp30) cc_final: 0.8101 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1598
  time to fit residues: 24.2046
Evaluate side-chains
  87 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0970
   chunk 39 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0270
   chunk 53 optimal weight:    0.0980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.2436

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  90 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5221  Z= 0.153
  Angle     :  0.598  10.764   7085  Z= 0.305
  Chirality :  0.042   0.145    789
  Planarity :  0.004   0.045    909
  Dihedral  :  5.147  28.143    725
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.98 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.32), residues: 642
  helix:  0.91 (0.75), residues: 48
  sheet: -0.21 (0.37), residues: 193
  loop : -1.37 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I 103 
 HIS   0.004   0.001   HIS I  35 
 PHE   0.013   0.001   PHE A 233 
 TYR   0.012   0.001   TYR J  49 
 ARG   0.005   0.001   ARG J  24 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8565 (p) cc_final: 0.8251 (t)
REVERT: A  116 LEU cc_start: 0.9640 (mm) cc_final: 0.9268 (mp)
REVERT: A  236 THR cc_start: 0.8187 (m) cc_final: 0.7966 (m)
REVERT: A  347 LYS cc_start: 0.8463 (pttt) cc_final: 0.8228 (tptp)
REVERT: A  396 MET cc_start: 0.6993 (ppp) cc_final: 0.6495 (ppp)
REVERT: A  426 MET cc_start: 0.6291 (tmm) cc_final: 0.5990 (tmm)
REVERT: A  434 MET cc_start: 0.7926 (ttm) cc_final: 0.7512 (tpp)
REVERT: I    3 HIS cc_start: 0.7994 (t-90) cc_final: 0.7517 (t-90)
REVERT: I    4 LEU cc_start: 0.8134 (mt) cc_final: 0.7785 (mt)
REVERT: I   47 TRP cc_start: 0.7705 (t-100) cc_final: 0.7093 (t-100)
REVERT: I   71 ARG cc_start: 0.8498 (ptt90) cc_final: 0.8055 (ptt90)
REVERT: I   80 MET cc_start: 0.9030 (ttt) cc_final: 0.8457 (ttp)
REVERT: I   89 VAL cc_start: 0.8045 (p) cc_final: 0.7821 (p)
REVERT: J   79 GLN cc_start: 0.8077 (pp30) cc_final: 0.7469 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1461
  time to fit residues: 21.9488
Evaluate side-chains
  85 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5221  Z= 0.342
  Angle     :  0.667   9.773   7085  Z= 0.346
  Chirality :  0.044   0.141    789
  Planarity :  0.004   0.043    909
  Dihedral  :  5.747  30.321    725
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.66 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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 (0.31), residues: 642
  helix:  0.74 (0.74), residues: 47
  sheet: -0.38 (0.37), residues: 193
  loop : -1.60 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP I  47 
 HIS   0.008   0.002   HIS I  35 
 PHE   0.014   0.002   PHE A  93 
 TYR   0.015   0.002   TYR I  32 
 ARG   0.005   0.001   ARG J  24 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8539 (p) cc_final: 0.8219 (t)
REVERT: A   93 PHE cc_start: 0.7240 (m-80) cc_final: 0.7039 (m-80)
REVERT: A  236 THR cc_start: 0.8317 (m) cc_final: 0.8094 (m)
REVERT: A  347 LYS cc_start: 0.8481 (pttt) cc_final: 0.8243 (tptp)
REVERT: A  396 MET cc_start: 0.7026 (ppp) cc_final: 0.6618 (ppp)
REVERT: A  426 MET cc_start: 0.6689 (tmm) cc_final: 0.6143 (tmm)
REVERT: A  434 MET cc_start: 0.8089 (ttm) cc_final: 0.7517 (tpp)
REVERT: I    3 HIS cc_start: 0.8110 (t-90) cc_final: 0.7826 (t-90)
REVERT: I    4 LEU cc_start: 0.8194 (mt) cc_final: 0.7799 (mt)
REVERT: I   52 ASN cc_start: 0.9492 (t0) cc_final: 0.9231 (t0)
REVERT: I   71 ARG cc_start: 0.8615 (ptt90) cc_final: 0.7902 (ptt90)
REVERT: I   80 MET cc_start: 0.8946 (ttt) cc_final: 0.8232 (ttp)
REVERT: J   79 GLN cc_start: 0.8043 (pp30) cc_final: 0.7322 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1486
  time to fit residues: 20.9219
Evaluate side-chains
  84 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0050
   chunk 31 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5221  Z= 0.165
  Angle     :  0.596  10.136   7085  Z= 0.305
  Chirality :  0.042   0.147    789
  Planarity :  0.003   0.045    909
  Dihedral  :  5.337  30.298    725
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.76 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.37 (0.32), residues: 642
  helix:  0.88 (0.75), residues: 48
  sheet: -0.19 (0.37), residues: 186
  loop : -1.56 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  50 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.012   0.001   PHE A 233 
 TYR   0.012   0.001   TYR J  49 
 ARG   0.004   0.001   ARG J  24 

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8573 (p) cc_final: 0.8251 (t)
REVERT: A  116 LEU cc_start: 0.9655 (mm) cc_final: 0.9264 (mp)
REVERT: A  236 THR cc_start: 0.8265 (m) cc_final: 0.8035 (m)
REVERT: A  347 LYS cc_start: 0.8442 (pttt) cc_final: 0.8219 (tptp)
REVERT: A  396 MET cc_start: 0.6924 (ppp) cc_final: 0.6496 (ppp)
REVERT: A  426 MET cc_start: 0.6488 (tmm) cc_final: 0.6143 (tmm)
REVERT: A  434 MET cc_start: 0.8018 (ttm) cc_final: 0.7489 (tpp)
REVERT: I    3 HIS cc_start: 0.8046 (t-90) cc_final: 0.7804 (t-90)
REVERT: I    4 LEU cc_start: 0.8232 (mt) cc_final: 0.7923 (mt)
REVERT: I   47 TRP cc_start: 0.8050 (t-100) cc_final: 0.7209 (t-100)
REVERT: I   71 ARG cc_start: 0.8666 (ptt90) cc_final: 0.7909 (ptt90)
REVERT: I   80 MET cc_start: 0.8936 (ttt) cc_final: 0.8326 (ttp)
REVERT: J   79 GLN cc_start: 0.7899 (pp30) cc_final: 0.7673 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1512
  time to fit residues: 22.5424
Evaluate side-chains
  83 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    0.0060
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0170
   overall best weight:    0.3634

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 195 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.141951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.118531 restraints weight = 11659.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.121869 restraints weight = 7590.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.124255 restraints weight = 5551.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
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   0.023   5221  Z= 0.159
  Angle     :  0.589   9.275   7085  Z= 0.302
  Chirality :  0.043   0.196    789
  Planarity :  0.003   0.045    909
  Dihedral  :  5.217  35.826    725
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.01 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.26 (0.32), residues: 642
  helix:  1.15 (0.77), residues: 47
  sheet: -0.10 (0.38), residues: 181
  loop : -1.49 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP I  50 
 HIS   0.012   0.001   HIS I  35 
 PHE   0.013   0.001   PHE A 233 
 TYR   0.013   0.001   TYR J  49 
 ARG   0.005   0.000   ARG J  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1544.28 seconds
wall clock time: 28 minutes 32.13 seconds (1712.13 seconds total)