Starting phenix.real_space_refine
on Tue Feb 11 10:33:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1d_41810/02_2025/8u1d_41810.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1d_41810/02_2025/8u1d_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/cci-nas-00/data/ceres_data/8u1d_41810/02_2025/8u1d_41810.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1d_41810/02_2025/8u1d_41810.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1d_41810/02_2025/8u1d_41810.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1d_41810/02_2025/8u1d_41810.cif"
  }
  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. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.78, per 1000 atoms: 0.74
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 386 "
  Time building additional restraints: 1.24
  Conformation dependent library (CDL) restraints added in 635.0 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: 0.76
  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: 1.67

  Time building geometry restraints manager: 1.45 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:
        0.00 -     1.85: 6546
        1.85 -     3.70: 447
        3.70 -     5.55: 58
        5.55 -     7.40: 24
        7.40 -     9.25: 10
  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 3.120
  nonbonded pdb=" OG  SER J  14 "
            pdb=" OD2 ASP J  17 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG  SER A 479 "
            pdb=" OE1 GLU A 480 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   PHE I 100E"
            pdb=" OH  TYR J  36 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   GLN J   3 "
            pdb=" OG  SER J  26 "
     model   vdw
     2.347 3.040
  ... (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
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:             2.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.730
  Find NCS groups from input model:        0.260
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.710
-------------------------------------------------------------------------------
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 to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.567 
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: 0.1653
  time to fit residues: 29.6423
Evaluate side-chains
  97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0170
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0670
   overall best weight:    0.3556

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.145690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.122129 restraints weight = 11639.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.125832 restraints weight = 7356.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.128502 restraints weight = 5214.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5221  Z= 0.158
  Angle     :  0.581   6.716   7085  Z= 0.312
  Chirality :  0.043   0.143    789
  Planarity :  0.005   0.053    909
  Dihedral  :  6.048  52.951    725
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.67 %
    Favored  : 95.17 %
  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: -1.58 (0.31), residues: 642
  helix: -0.73 (0.68), residues: 52
  sheet: -0.40 (0.38), residues: 169
  loop : -1.43 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP I  50 
 HIS   0.005   0.001   HIS I  35 
 PHE   0.014   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 to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8659 (p) cc_final: 0.8380 (t)
REVERT: A  122 LEU cc_start: 0.9139 (tp) cc_final: 0.8924 (tp)
REVERT: A  145 MET cc_start: 0.2189 (mtt) cc_final: 0.1832 (mtt)
REVERT: A  396 MET cc_start: 0.6720 (ppp) cc_final: 0.6304 (ppp)
REVERT: A  426 MET cc_start: 0.7171 (tmm) cc_final: 0.6699 (tmm)
REVERT: I    3 HIS cc_start: 0.8034 (t-90) cc_final: 0.7615 (t-90)
REVERT: I   80 MET cc_start: 0.8953 (ttt) cc_final: 0.8529 (ttp)
REVERT: J    2 ILE cc_start: 0.8051 (mp) cc_final: 0.7498 (mp)
REVERT: J   79 GLN cc_start: 0.8066 (pp30) cc_final: 0.7646 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1630
  time to fit residues: 25.8580
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0970
   chunk 11 optimal weight:    0.0980
   chunk 52 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0770
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.3136

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.146186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.122462 restraints weight = 11819.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.126096 restraints weight = 7656.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.128795 restraints weight = 5521.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5221  Z= 0.148
  Angle     :  0.568   6.027   7085  Z= 0.305
  Chirality :  0.043   0.177    789
  Planarity :  0.004   0.059    909
  Dihedral  :  5.892  59.278    725
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.45 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  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: -1.40 (0.32), residues: 642
  helix: -0.26 (0.73), residues: 52
  sheet: -0.17 (0.38), residues: 184
  loop : -1.45 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I  50 
 HIS   0.003   0.001   HIS I  35 
 PHE   0.031   0.001   PHE J  83 
 TYR   0.015   0.001   TYR A 330 
 ARG   0.005   0.000   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
  114 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8693 (p) cc_final: 0.8413 (t)
REVERT: A  104 MET cc_start: 0.8092 (tpp) cc_final: 0.7293 (tpp)
REVERT: A  321 GLN cc_start: 0.8354 (mp-120) cc_final: 0.8071 (pm20)
REVERT: A  396 MET cc_start: 0.6820 (ppp) cc_final: 0.6421 (ppp)
REVERT: A  426 MET cc_start: 0.7053 (tmm) cc_final: 0.6535 (tmm)
REVERT: A  434 MET cc_start: 0.8180 (ttm) cc_final: 0.7765 (tpp)
REVERT: I    3 HIS cc_start: 0.8028 (t-90) cc_final: 0.7600 (t-90)
REVERT: I   71 ARG cc_start: 0.8941 (ppt170) cc_final: 0.8579 (ptt90)
REVERT: I   80 MET cc_start: 0.8975 (ttt) cc_final: 0.8738 (ttp)
REVERT: I  100 SER cc_start: 0.7972 (p) cc_final: 0.7655 (p)
REVERT: J    2 ILE cc_start: 0.8139 (mp) cc_final: 0.7820 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1674
  time to fit residues: 25.1496
Evaluate side-chains
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 55 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.135401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.112347 restraints weight = 12195.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.115423 restraints weight = 7904.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.117646 restraints weight = 5827.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5221  Z= 0.401
  Angle     :  0.722   6.429   7085  Z= 0.386
  Chirality :  0.045   0.182    789
  Planarity :  0.005   0.056    909
  Dihedral  :  6.600  57.189    725
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.72 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  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: -1.39 (0.32), residues: 642
  helix:  0.37 (0.73), residues: 47
  sheet: -0.44 (0.37), residues: 198
  loop : -1.38 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP I  47 
 HIS   0.006   0.001   HIS I  58 
 PHE   0.018   0.003   PHE A 233 
 TYR   0.023   0.003   TYR I  32 
 ARG   0.004   0.001   ARG A 344 

*********************** 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
  108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.565 
Fit side-chains
REVERT: A   77 THR cc_start: 0.8763 (p) cc_final: 0.8519 (t)
REVERT: A   93 PHE cc_start: 0.7118 (m-80) cc_final: 0.6839 (m-80)
REVERT: A  426 MET cc_start: 0.7217 (tmm) cc_final: 0.6361 (tmm)
REVERT: I    3 HIS cc_start: 0.8259 (t-90) cc_final: 0.7865 (t-90)
REVERT: I    4 LEU cc_start: 0.8473 (mt) cc_final: 0.8102 (mt)
REVERT: I   13 GLU cc_start: 0.8364 (mp0) cc_final: 0.8105 (mp0)
REVERT: I   53 TYR cc_start: 0.8376 (t80) cc_final: 0.8156 (t80)
REVERT: I   80 MET cc_start: 0.9080 (ttt) cc_final: 0.8526 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1594
  time to fit residues: 22.7673
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0870
   chunk 5 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.140898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.117947 restraints weight = 11713.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.121360 restraints weight = 7443.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.123815 restraints weight = 5347.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.2646

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= 0.193
  Angle     :  0.611   5.829   7085  Z= 0.324
  Chirality :  0.043   0.153    789
  Planarity :  0.004   0.051    909
  Dihedral  :  5.917  46.899    725
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.30 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  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: -1.25 (0.32), residues: 642
  helix:  0.64 (0.75), residues: 47
  sheet: -0.23 (0.36), residues: 203
  loop : -1.39 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 249 
 PHE   0.033   0.002   PHE J  83 
 TYR   0.019   0.002   TYR A 435 
 ARG   0.003   0.000   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
  111 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8761 (p) cc_final: 0.8533 (t)
REVERT: A  104 MET cc_start: 0.8888 (tpp) cc_final: 0.7805 (tpp)
REVERT: A  347 LYS cc_start: 0.8357 (pttt) cc_final: 0.8073 (tptp)
REVERT: A  396 MET cc_start: 0.6553 (ppp) cc_final: 0.6227 (ppp)
REVERT: A  426 MET cc_start: 0.7083 (tmm) cc_final: 0.6702 (tmm)
REVERT: I    3 HIS cc_start: 0.8179 (t-90) cc_final: 0.7857 (t-90)
REVERT: I    4 LEU cc_start: 0.8377 (mt) cc_final: 0.8088 (mt)
REVERT: I   13 GLU cc_start: 0.8321 (mp0) cc_final: 0.8028 (mp0)
REVERT: I   71 ARG cc_start: 0.8921 (ppt170) cc_final: 0.8428 (ptt90)
REVERT: I   80 MET cc_start: 0.9117 (ttt) cc_final: 0.8618 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1711
  time to fit residues: 25.3436
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0770
   chunk 12 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0470
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0470
   chunk 47 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.3534

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 103 GLN
A 195 ASN
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.142545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.118906 restraints weight = 11663.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.122372 restraints weight = 7435.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.124831 restraints weight = 5359.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2730

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= 0.172
  Angle     :  0.611   9.243   7085  Z= 0.320
  Chirality :  0.043   0.158    789
  Planarity :  0.004   0.050    909
  Dihedral  :  5.604  36.002    725
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.07 %
    Favored  : 93.77 %
  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: -1.42 (0.32), residues: 642
  helix: -0.05 (0.70), residues: 54
  sheet: -0.19 (0.37), residues: 203
  loop : -1.55 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I 103 
 HIS   0.004   0.001   HIS A 249 
 PHE   0.015   0.001   PHE A 233 
 TYR   0.011   0.001   TYR J  91 
 ARG   0.006   0.000   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
  105 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8759 (p) cc_final: 0.8529 (t)
REVERT: A  104 MET cc_start: 0.8073 (tpp) cc_final: 0.7478 (tpt)
REVERT: A  347 LYS cc_start: 0.8362 (pttt) cc_final: 0.8084 (tptp)
REVERT: A  396 MET cc_start: 0.6483 (ppp) cc_final: 0.6173 (ppp)
REVERT: A  426 MET cc_start: 0.7010 (tmm) cc_final: 0.6744 (tmm)
REVERT: A  434 MET cc_start: 0.8164 (ttm) cc_final: 0.7922 (tpp)
REVERT: I    3 HIS cc_start: 0.8177 (t-90) cc_final: 0.7823 (t-90)
REVERT: I    4 LEU cc_start: 0.8347 (mt) cc_final: 0.8082 (mt)
REVERT: I   80 MET cc_start: 0.9120 (ttt) cc_final: 0.8650 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1695
  time to fit residues: 23.3716
Evaluate side-chains
  83 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 103 GLN
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 ASN
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.139432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114012 restraints weight = 12416.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.117609 restraints weight = 8001.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.120238 restraints weight = 5825.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5221  Z= 0.225
  Angle     :  0.624  10.794   7085  Z= 0.325
  Chirality :  0.043   0.148    789
  Planarity :  0.004   0.049    909
  Dihedral  :  5.566  30.674    725
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.23 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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: -1.48 (0.32), residues: 642
  helix:  0.28 (0.71), residues: 53
  sheet: -0.27 (0.37), residues: 198
  loop : -1.62 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I  50 
 HIS   0.005   0.001   HIS I  35 
 PHE   0.013   0.001   PHE A 233 
 TYR   0.012   0.001   TYR J  91 
 ARG   0.007   0.001   ARG J  24 

*********************** 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
  108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8749 (p) cc_final: 0.8465 (t)
REVERT: A  347 LYS cc_start: 0.8464 (pttt) cc_final: 0.8193 (tptp)
REVERT: A  396 MET cc_start: 0.6685 (ppp) cc_final: 0.6343 (ppp)
REVERT: A  426 MET cc_start: 0.7027 (tmm) cc_final: 0.6764 (tmm)
REVERT: A  434 MET cc_start: 0.8206 (ttm) cc_final: 0.7851 (tpp)
REVERT: I    3 HIS cc_start: 0.8139 (t-90) cc_final: 0.7699 (t-90)
REVERT: I    4 LEU cc_start: 0.8314 (mt) cc_final: 0.7973 (mt)
REVERT: I   13 GLU cc_start: 0.8527 (mp0) cc_final: 0.8276 (mp0)
REVERT: I   47 TRP cc_start: 0.7577 (t-100) cc_final: 0.6979 (t-100)
REVERT: I   80 MET cc_start: 0.9040 (ttt) cc_final: 0.8496 (ttp)
REVERT: J   79 GLN cc_start: 0.8095 (pp30) cc_final: 0.7779 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1729
  time to fit residues: 24.0539
Evaluate side-chains
  84 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 34 optimal weight:    0.0070
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0060
   chunk 3 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 20 optimal weight:    0.1980
   chunk 7 optimal weight:    0.2980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.2214

-------------------------------------------------------------------------------
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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.143638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.120665 restraints weight = 11579.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.124234 restraints weight = 7270.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.126765 restraints weight = 5185.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5221  Z= 0.162
  Angle     :  0.618  11.988   7085  Z= 0.320
  Chirality :  0.043   0.149    789
  Planarity :  0.004   0.049    909
  Dihedral  :  5.131  27.388    725
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.83 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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: -1.37 (0.32), residues: 642
  helix:  0.45 (0.71), residues: 53
  sheet: -0.13 (0.37), residues: 198
  loop : -1.59 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP I 103 
 HIS   0.005   0.001   HIS I  35 
 PHE   0.015   0.001   PHE A 233 
 TYR   0.013   0.001   TYR J  49 
 ARG   0.006   0.001   ARG J  42 

*********************** 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
  110 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8856 (p) cc_final: 0.8631 (t)
REVERT: A  347 LYS cc_start: 0.8336 (pttt) cc_final: 0.8084 (tptp)
REVERT: A  396 MET cc_start: 0.6603 (ppp) cc_final: 0.6318 (ppp)
REVERT: I    3 HIS cc_start: 0.8075 (t-90) cc_final: 0.7743 (t-90)
REVERT: I    4 LEU cc_start: 0.8409 (mt) cc_final: 0.8115 (mt)
REVERT: I   13 GLU cc_start: 0.8315 (mp0) cc_final: 0.8098 (mp0)
REVERT: I   46 GLU cc_start: 0.7451 (tp30) cc_final: 0.7192 (tp30)
REVERT: I   47 TRP cc_start: 0.7649 (t-100) cc_final: 0.7116 (t-100)
REVERT: I   59 TYR cc_start: 0.8979 (m-10) cc_final: 0.8532 (m-10)
REVERT: I   80 MET cc_start: 0.9140 (ttt) cc_final: 0.8693 (ttp)
REVERT: J   38 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7495 (tp40)
REVERT: J   79 GLN cc_start: 0.8036 (pp30) cc_final: 0.7803 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1632
  time to fit residues: 23.5182
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    0.2980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.141641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.119229 restraints weight = 11700.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.122704 restraints weight = 7283.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.125156 restraints weight = 5145.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5221  Z= 0.172
  Angle     :  0.617  11.538   7085  Z= 0.314
  Chirality :  0.043   0.146    789
  Planarity :  0.004   0.049    909
  Dihedral  :  5.015  28.203    725
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.61 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  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: -1.33 (0.32), residues: 642
  helix:  0.35 (0.70), residues: 54
  sheet: -0.06 (0.38), residues: 191
  loop : -1.55 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 249 
 PHE   0.011   0.001   PHE A 233 
 TYR   0.018   0.001   TYR A 435 
 ARG   0.006   0.000   ARG J  42 

*********************** 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
  109 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8842 (p) cc_final: 0.8614 (t)
REVERT: A  116 LEU cc_start: 0.9483 (mm) cc_final: 0.9217 (mt)
REVERT: A  347 LYS cc_start: 0.8330 (pttt) cc_final: 0.8089 (tptp)
REVERT: A  396 MET cc_start: 0.6626 (ppp) cc_final: 0.6352 (ppp)
REVERT: A  426 MET cc_start: 0.7010 (tmm) cc_final: 0.6502 (tmm)
REVERT: I    4 LEU cc_start: 0.8417 (mt) cc_final: 0.8146 (mt)
REVERT: I   46 GLU cc_start: 0.7486 (tp30) cc_final: 0.7136 (tp30)
REVERT: I   47 TRP cc_start: 0.7745 (t-100) cc_final: 0.7202 (t-100)
REVERT: I   80 MET cc_start: 0.9079 (ttt) cc_final: 0.8615 (ttp)
REVERT: I   96 GLU cc_start: 0.7292 (tt0) cc_final: 0.6802 (mt-10)
REVERT: J   79 GLN cc_start: 0.8077 (pp30) cc_final: 0.7673 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1652
  time to fit residues: 23.6514
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 43 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0060
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.141525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.118580 restraints weight = 11636.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.122034 restraints weight = 7307.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.124522 restraints weight = 5225.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5221  Z= 0.188
  Angle     :  0.624  11.457   7085  Z= 0.321
  Chirality :  0.043   0.147    789
  Planarity :  0.004   0.048    909
  Dihedral  :  5.050  28.981    725
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.92 %
    Favored  : 93.93 %
  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 : 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: -1.31 (0.32), residues: 642
  helix:  0.39 (0.70), residues: 54
  sheet: -0.17 (0.37), residues: 198
  loop : -1.48 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP I  50 
 HIS   0.005   0.001   HIS I  35 
 PHE   0.010   0.001   PHE A 233 
 TYR   0.012   0.001   TYR J  91 
 ARG   0.007   0.000   ARG J  42 

********************** 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
  114 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8788 (p) cc_final: 0.8587 (t)
REVERT: A  116 LEU cc_start: 0.9518 (mm) cc_final: 0.9262 (mt)
REVERT: A  347 LYS cc_start: 0.8334 (pttt) cc_final: 0.8119 (tptp)
REVERT: A  396 MET cc_start: 0.6586 (ppp) cc_final: 0.6322 (ppp)
REVERT: A  426 MET cc_start: 0.6881 (tmm) cc_final: 0.6363 (tmm)
REVERT: I    4 LEU cc_start: 0.8343 (mt) cc_final: 0.8127 (mt)
REVERT: I   13 GLU cc_start: 0.8328 (mp0) cc_final: 0.8103 (mp0)
REVERT: I   47 TRP cc_start: 0.7997 (t-100) cc_final: 0.7482 (t-100)
REVERT: I   80 MET cc_start: 0.9094 (ttt) cc_final: 0.8622 (ttp)
REVERT: I   89 VAL cc_start: 0.8010 (p) cc_final: 0.7687 (p)
REVERT: J   79 GLN cc_start: 0.8056 (pp30) cc_final: 0.7790 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1714
  time to fit residues: 25.9136
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0470
   chunk 57 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0470
   chunk 50 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 5 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.3176

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.142442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.119828 restraints weight = 11741.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.123283 restraints weight = 7394.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.125821 restraints weight = 5259.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5221  Z= 0.156
  Angle     :  0.600  10.403   7085  Z= 0.309
  Chirality :  0.043   0.149    789
  Planarity :  0.003   0.049    909
  Dihedral  :  4.885  29.269    725
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.67 %
    Favored  : 95.17 %
  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 : 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: -1.32 (0.32), residues: 642
  helix: -0.01 (0.69), residues: 59
  sheet: -0.03 (0.38), residues: 191
  loop : -1.51 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  50 
 HIS   0.006   0.001   HIS I  35 
 PHE   0.009   0.001   PHE A 233 
 TYR   0.012   0.001   TYR J  91 
 ARG   0.006   0.000   ARG J  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1959.70 seconds
wall clock time: 35 minutes 51.54 seconds (2151.54 seconds total)