Starting phenix.real_space_refine
on Fri Oct 10 20:16:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u58_41914/10_2025/8u58_41914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u58_41914/10_2025/8u58_41914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u58_41914/10_2025/8u58_41914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u58_41914/10_2025/8u58_41914.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u58_41914/10_2025/8u58_41914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u58_41914/10_2025/8u58_41914.map"
  }
  resolution = 2.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.027
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      56      5.16       5
     C    5962      2.51       5
     N    1362      2.21       5
     O    1504      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8884
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 4428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4428
          Classifications: {'peptide': 565}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 544}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      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
  Restraints were copied for chains:
    A
  Time building chain proxies: 3.62, per 1000 atoms: 0.41
  Number of scatterers: 8884
  At special positions: 0
  Unit cell: (130.491, 99.5598, 69.5952, 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      56     16.00
     O    1504      8.00
     N    1362      7.00
     C    5962      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 309 "
      " NAG C 901 " - " ASN C 309 "
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 287.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      89.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'C' and resid 38 through 40
      No H-bonds generated for 'chain 'C' and resid 38 through 40'
    Processing helix  chain 'C' and resid 41 through 62
    Processing helix  chain 'C' and resid 66 through 80
      removed outlier: 3.612A  pdb=" N   LYS C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLY C  72 " --> pdb=" O   THR C  68 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU C  73 " --> pdb=" O   GLN C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 93
    Processing helix  chain 'C' and resid 94 through 98
      removed outlier: 3.508A  pdb=" N   VAL C  98 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 125
    Processing helix  chain 'C' and resid 129 through 141
      Proline residue:  C 138  - end of helix
    Processing helix  chain 'C' and resid 149 through 159
      removed outlier: 3.507A  pdb=" N   ILE C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 165
    Processing helix  chain 'C' and resid 166 through 196
      removed outlier: 4.134A  pdb=" N   TYR C 170 " --> pdb=" O   LEU C 166 " (cutoff:3.500A)
      Proline residue:  C 174  - end of helix
      Proline residue:  C 182  - end of helix
    Processing helix  chain 'C' and resid 202 through 216
    Processing helix  chain 'C' and resid 217 through 233
      removed outlier: 3.587A  pdb=" N   VAL C 223 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 264
      removed outlier: 4.223A  pdb=" N   ASN C 243 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   PHE C 244 " --> pdb=" O   TYR C 240 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   SER C 253 " --> pdb=" O   GLY C 249 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   GLY C 254 " --> pdb=" O   ASN C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 288
    Processing helix  chain 'C' and resid 288 through 302
    Processing helix  chain 'C' and resid 306 through 322
    Processing helix  chain 'C' and resid 326 through 337
      removed outlier: 4.170A  pdb=" N   ALA C 330 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 367
      removed outlier: 3.673A  pdb=" N   ALA C 355 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
      Proline residue:  C 356  - end of helix
    Processing helix  chain 'C' and resid 368 through 370
      No H-bonds generated for 'chain 'C' and resid 368 through 370'
    Processing helix  chain 'C' and resid 371 through 404
    Processing helix  chain 'C' and resid 405 through 409
    Processing helix  chain 'C' and resid 411 through 436
      removed outlier: 4.101A  pdb=" N   PHE C 434 " --> pdb=" O   MET C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 472
      removed outlier: 3.914A  pdb=" N   LEU C 445 " --> pdb=" O   VAL C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 503
      removed outlier: 4.197A  pdb=" N   ILE C 491 " --> pdb=" O   SER C 487 " (cutoff:3.500A)
      Proline residue:  C 492  - end of helix
    Processing helix  chain 'C' and resid 511 through 515
    Processing helix  chain 'C' and resid 516 through 542
    Processing helix  chain 'C' and resid 654 through 682
    Processing helix  chain 'C' and resid 688 through 712
      removed outlier: 5.656A  pdb=" N   GLY C 704 " --> pdb=" O   ASN C 700 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   PHE C 705 " --> pdb=" O   PHE C 701 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE C 706 " --> pdb=" O   GLY C 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 62
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 3.603A  pdb=" N   LYS A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLY A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 93
    Processing helix  chain 'A' and resid 94 through 98
      removed outlier: 3.522A  pdb=" N   VAL A  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 125
    Processing helix  chain 'A' and resid 129 through 141
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.505A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 165
    Processing helix  chain 'A' and resid 166 through 196
      removed outlier: 4.134A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 202 through 216
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.582A  pdb=" N   VAL A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 264
      removed outlier: 4.219A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   SER A 253 " --> pdb=" O   GLY A 249 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   GLY A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 322
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 4.176A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.681A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 368 through 370
      No H-bonds generated for 'chain 'A' and resid 368 through 370'
    Processing helix  chain 'A' and resid 371 through 404
    Processing helix  chain 'A' and resid 405 through 409
    Processing helix  chain 'A' and resid 411 through 436
      removed outlier: 4.099A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 472
      removed outlier: 3.911A  pdb=" N   LEU A 445 " --> pdb=" O   VAL A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 503
      removed outlier: 4.196A  pdb=" N   ILE A 491 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
    Processing helix  chain 'A' and resid 516 through 542
    Processing helix  chain 'A' and resid 654 through 682
    Processing helix  chain 'A' and resid 688 through 712
      removed outlier: 5.652A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)

    732 hydrogen bonds defined for protein.
    2160 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: 1.45

  Time building geometry restraints manager: 1.46 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: 2350
        1.34 -     1.45: 1673
        1.45 -     1.57: 4981
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 9094
  Sorted by residual:
  bond pdb=" C1  NAG A 901 "
       pdb=" O5  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.45e+00
  bond pdb=" C1  NAG C 901 "
       pdb=" O5  NAG C 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 6.12e+00
  bond pdb=" CB  TYR C 320 "
       pdb=" CG  TYR C 320 "
    ideal  model  delta    sigma   weight residual
    1.512  1.465  0.047 2.20e-02 2.07e+03 4.59e+00
  bond pdb=" CB  TYR A 320 "
       pdb=" CG  TYR A 320 "
    ideal  model  delta    sigma   weight residual
    1.512  1.465  0.047 2.20e-02 2.07e+03 4.49e+00
  bond pdb=" C   PRO A 372 "
       pdb=" N   LYS A 373 "
    ideal  model  delta    sigma   weight residual
    1.337  1.305  0.032 1.61e-02 3.86e+03 4.03e+00
  ... (remaining 9089 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 11528
        1.89 -     3.78: 708
        3.78 -     5.68: 92
        5.68 -     7.57: 18
        7.57 -     9.46: 10
  Bond angle restraints: 12356
  Sorted by residual:
  angle pdb=" CA  TYR C 451 "
        pdb=" CB  TYR C 451 "
        pdb=" CG  TYR C 451 "
      ideal   model   delta    sigma   weight residual
     113.90  104.44    9.46 1.80e+00 3.09e-01 2.76e+01
  angle pdb=" CA  TYR A 451 "
        pdb=" CB  TYR A 451 "
        pdb=" CG  TYR A 451 "
      ideal   model   delta    sigma   weight residual
     113.90  104.47    9.43 1.80e+00 3.09e-01 2.75e+01
  angle pdb=" CA  TYR A 689 "
        pdb=" CB  TYR A 689 "
        pdb=" CG  TYR A 689 "
      ideal   model   delta    sigma   weight residual
     113.90  106.06    7.84 1.80e+00 3.09e-01 1.90e+01
  angle pdb=" CA  TYR C 689 "
        pdb=" CB  TYR C 689 "
        pdb=" CG  TYR C 689 "
      ideal   model   delta    sigma   weight residual
     113.90  106.08    7.82 1.80e+00 3.09e-01 1.89e+01
  angle pdb=" CA  TYR C 320 "
        pdb=" CB  TYR C 320 "
        pdb=" CG  TYR C 320 "
      ideal   model   delta    sigma   weight residual
     113.90  106.76    7.14 1.80e+00 3.09e-01 1.57e+01
  ... (remaining 12351 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 4953
       16.92 -    33.83: 323
       33.83 -    50.75: 36
       50.75 -    67.66: 10
       67.66 -    84.58: 4
  Dihedral angle restraints: 5326
    sinusoidal: 2050
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" CA  ASN A  63 "
           pdb=" C   ASN A  63 "
           pdb=" N   VAL A  64 "
           pdb=" CA  VAL A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.15   22.85     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASN C  63 "
           pdb=" C   ASN C  63 "
           pdb=" N   VAL C  64 "
           pdb=" CA  VAL C  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.24   22.76     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  MET A 179 "
           pdb=" C   MET A 179 "
           pdb=" N   LEU A 180 "
           pdb=" CA  LEU A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.59  -20.41     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 964
       0.046 -    0.091: 419
       0.091 -    0.137: 92
       0.137 -    0.183: 21
       0.183 -    0.228: 6
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" C1  NAG C 901 "
            pdb=" ND2 ASN C 309 "
            pdb=" C2  NAG C 901 "
            pdb=" O5  NAG C 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" C1  NAG A 901 "
            pdb=" ND2 ASN A 309 "
            pdb=" C2  NAG A 901 "
            pdb=" O5  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  TYR C 451 "
            pdb=" N   TYR C 451 "
            pdb=" C   TYR C 451 "
            pdb=" CB  TYR C 451 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1499 not shown)

  Planarity restraints: 1478
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 320 "    0.096 2.00e-02 2.50e+03   4.85e-02 4.71e+01
        pdb=" CG  TYR C 320 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 320 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 320 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 320 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 320 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 320 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR C 320 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 320 "   -0.096 2.00e-02 2.50e+03   4.85e-02 4.70e+01
        pdb=" CG  TYR A 320 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 320 "    0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 320 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 320 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 320 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 320 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 320 "   -0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 901 "   -0.066 2.00e-02 2.50e+03   5.47e-02 3.74e+01
        pdb=" C7  NAG A 901 "    0.004 2.00e-02 2.50e+03
        pdb=" C8  NAG A 901 "   -0.046 2.00e-02 2.50e+03
        pdb=" N2  NAG A 901 "    0.091 2.00e-02 2.50e+03
        pdb=" O7  NAG A 901 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1475 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 4804
        2.99 -     3.47: 10323
        3.47 -     3.95: 16113
        3.95 -     4.42: 19101
        4.42 -     4.90: 29395
  Nonbonded interactions: 79736
  Sorted by model distance:
  nonbonded pdb=" O   SER A 101 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.518 3.040
  nonbonded pdb=" O   SER C 101 "
            pdb=" OG  SER C 105 "
     model   vdw
     2.519 3.040
  nonbonded pdb=" OE2 GLU A 299 "
            pdb=" OG  SER A 314 "
     model   vdw
     2.545 3.040
  nonbonded pdb=" O   ILE C 400 "
            pdb=" OG  SER C 404 "
     model   vdw
     2.545 3.040
  nonbonded pdb=" O   ILE A 400 "
            pdb=" OG  SER A 404 "
     model   vdw
     2.546 3.040
  ... (remaining 79731 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     11.420
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
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      :  0.007   0.052   9096  Z= 0.365
  Angle     :  1.061   9.462  12362  Z= 0.604
  Chirality :  0.053   0.228   1502
  Planarity :  0.009   0.095   1476
  Dihedral  : 11.796  84.578   3210
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.22), residues: 1110
  helix: -0.36 (0.15), residues: 902
  sheet:  None (None), residues: 0
  loop : -0.19 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 687 
 TYR   0.096   0.009   TYR A 320 
 PHE   0.054   0.007   PHE A 694 
 TRP   0.031   0.006   TRP A 100 
 HIS   0.007   0.003   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00737 ( 9094)
  covalent geometry    : angle       1.05572 (12356)
  hydrogen bonds       : bond        0.11708 (  732)
  hydrogen bonds       : angle       6.64466 ( 2160)
  link_NAG-ASN         : bond        0.00968 (    2)
  link_NAG-ASN         : angle       5.06188 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A  193 TRP cc_start: 0.6946 (t-100) cc_final: 0.6717 (t-100)
  outliers start: 0
  outliers final: 1
  residues processed: 202
  average time/residue: 0.4804
  time to fit residues: 104.6237
Evaluate side-chains
  78 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  710 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
C 143 GLN
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 167 GLN
** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 654 GLN
** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 143 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 167 GLN
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.132397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.097133 restraints weight = 16871.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.27
r_work: 0.3355 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   9096  Z= 0.223
  Angle     :  0.708   8.569  12362  Z= 0.365
  Chirality :  0.046   0.155   1502
  Planarity :  0.005   0.035   1476
  Dihedral  :  4.962  33.992   1224
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  :  9.65 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.25), residues: 1110
  helix:  1.46 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.41 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 295 
 TYR   0.028   0.002   TYR C 455 
 PHE   0.020   0.002   PHE C 221 
 TRP   0.012   0.002   TRP C 396 
 HIS   0.004   0.001   HIS C 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 9094)
  covalent geometry    : angle       0.70614 (12356)
  hydrogen bonds       : bond        0.05446 (  732)
  hydrogen bonds       : angle       4.99358 ( 2160)
  link_NAG-ASN         : bond        0.00259 (    2)
  link_NAG-ASN         : angle       2.38624 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: C  130 ARG cc_start: 0.7917 (ptt180) cc_final: 0.7676 (ptp90)
REVERT: C  242 GLU cc_start: 0.8309 (tp30) cc_final: 0.8059 (tp30)
REVERT: C  352 PHE cc_start: 0.6696 (m-80) cc_final: 0.6018 (t80)
REVERT: C  401 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7332 (tp)
REVERT: A   37 MET cc_start: 0.7654 (ttm) cc_final: 0.7302 (ttm)
REVERT: A  130 ARG cc_start: 0.7906 (ptt180) cc_final: 0.7658 (ptp90)
REVERT: A  193 TRP cc_start: 0.8230 (t-100) cc_final: 0.7779 (t-100)
REVERT: A  242 GLU cc_start: 0.8329 (tp30) cc_final: 0.8063 (tp30)
REVERT: A  347 MET cc_start: 0.8516 (ttp) cc_final: 0.8307 (ttp)
REVERT: A  352 PHE cc_start: 0.6767 (m-10) cc_final: 0.6061 (t80)
REVERT: A  401 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7246 (tp)
REVERT: A  429 MET cc_start: 0.7157 (tpt) cc_final: 0.6897 (tpp)
REVERT: A  540 MET cc_start: 0.6302 (mmm) cc_final: 0.5970 (tmt)
  outliers start: 28
  outliers final: 5
  residues processed: 131
  average time/residue: 0.4487
  time to fit residues: 64.0245
Evaluate side-chains
  85 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  401 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 145 ASN
** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 658 HIS ** 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 = 0.4089 r_free = 0.4089 target = 0.131698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.095565 restraints weight = 16891.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.32
r_work: 0.3351 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.6069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9096  Z= 0.169
  Angle     :  0.632  11.671  12362  Z= 0.315
  Chirality :  0.042   0.153   1502
  Planarity :  0.004   0.036   1476
  Dihedral  :  4.614  31.726   1222
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 10.37 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.25), residues: 1110
  helix:  1.93 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.71 (0.46), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 235 
 TYR   0.033   0.002   TYR C 455 
 PHE   0.025   0.002   PHE A 221 
 TRP   0.008   0.001   TRP C 363 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9094)
  covalent geometry    : angle       0.63089 (12356)
  hydrogen bonds       : bond        0.05035 (  732)
  hydrogen bonds       : angle       4.66934 ( 2160)
  link_NAG-ASN         : bond        0.00318 (    2)
  link_NAG-ASN         : angle       1.60539 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.397 
Fit side-chains
REVERT: C  145 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8963 (t0)
REVERT: C  234 ASP cc_start: 0.8073 (m-30) cc_final: 0.7369 (t0)
REVERT: C  352 PHE cc_start: 0.6780 (m-80) cc_final: 0.6209 (t80)
REVERT: C  401 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7461 (tp)
REVERT: C  452 SER cc_start: 0.9033 (t) cc_final: 0.8627 (p)
REVERT: C  519 GLU cc_start: 0.7796 (mm-30) cc_final: 0.6958 (mp0)
REVERT: C  540 MET cc_start: 0.6397 (mmm) cc_final: 0.6117 (tmt)
REVERT: A   37 MET cc_start: 0.7899 (ttm) cc_final: 0.7561 (ttp)
REVERT: A  193 TRP cc_start: 0.8236 (t-100) cc_final: 0.7950 (m-90)
REVERT: A  234 ASP cc_start: 0.8015 (m-30) cc_final: 0.7331 (t0)
REVERT: A  299 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8190 (mt-10)
REVERT: A  338 MET cc_start: 0.8350 (mtt) cc_final: 0.8024 (mtm)
REVERT: A  352 PHE cc_start: 0.6788 (m-10) cc_final: 0.6229 (t80)
REVERT: A  401 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7445 (tp)
REVERT: A  429 MET cc_start: 0.7404 (tpt) cc_final: 0.7129 (tpt)
REVERT: A  519 GLU cc_start: 0.7822 (mm-30) cc_final: 0.6907 (mp0)
REVERT: A  540 MET cc_start: 0.6495 (mmm) cc_final: 0.6272 (tmt)
  outliers start: 28
  outliers final: 7
  residues processed: 119
  average time/residue: 0.4679
  time to fit residues: 60.3063
Evaluate side-chains
  80 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  145 ASN
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  401 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 75 optimal weight:    0.3980
   chunk 23 optimal weight:    0.4980
   chunk 80 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 412 HIS
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 412 HIS
A 658 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.131319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.095069 restraints weight = 17217.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.34
r_work: 0.3342 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.6694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9096  Z= 0.158
  Angle     :  0.585   9.617  12362  Z= 0.294
  Chirality :  0.041   0.146   1502
  Planarity :  0.004   0.034   1476
  Dihedral  :  4.414  29.923   1222
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.08 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.25), residues: 1110
  helix:  2.11 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.65 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 295 
 TYR   0.020   0.001   TYR C 455 
 PHE   0.023   0.002   PHE A 221 
 TRP   0.008   0.001   TRP C 396 
 HIS   0.004   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9094)
  covalent geometry    : angle       0.58389 (12356)
  hydrogen bonds       : bond        0.04764 (  732)
  hydrogen bonds       : angle       4.54509 ( 2160)
  link_NAG-ASN         : bond        0.00451 (    2)
  link_NAG-ASN         : angle       1.40102 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.432 
Fit side-chains
REVERT: C  193 TRP cc_start: 0.8113 (t-100) cc_final: 0.7877 (m-90)
REVERT: C  352 PHE cc_start: 0.6706 (m-10) cc_final: 0.6027 (t80)
REVERT: C  452 SER cc_start: 0.9048 (t) cc_final: 0.8658 (p)
REVERT: C  540 MET cc_start: 0.6597 (mmm) cc_final: 0.6275 (tmt)
REVERT: A  193 TRP cc_start: 0.8243 (t-100) cc_final: 0.7973 (m-90)
REVERT: A  338 MET cc_start: 0.8567 (mtt) cc_final: 0.8214 (mtm)
REVERT: A  352 PHE cc_start: 0.6708 (m-10) cc_final: 0.6027 (t80)
REVERT: A  452 SER cc_start: 0.9036 (t) cc_final: 0.8620 (p)
REVERT: A  540 MET cc_start: 0.6412 (mmm) cc_final: 0.6207 (tmt)
  outliers start: 20
  outliers final: 5
  residues processed: 96
  average time/residue: 0.4131
  time to fit residues: 43.4504
Evaluate side-chains
  80 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0270
   chunk 76 optimal weight:    0.3980
   chunk 111 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7840

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.131010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.094932 restraints weight = 17164.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.33
r_work: 0.3331 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.7212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9096  Z= 0.156
  Angle     :  0.589   9.695  12362  Z= 0.291
  Chirality :  0.042   0.260   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.341  28.370   1222
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  :  9.65 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.79 (0.25), residues: 1110
  helix:  2.13 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.75 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 235 
 TYR   0.021   0.001   TYR C 455 
 PHE   0.023   0.002   PHE A 221 
 TRP   0.007   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9094)
  covalent geometry    : angle       0.58853 (12356)
  hydrogen bonds       : bond        0.04678 (  732)
  hydrogen bonds       : angle       4.52454 ( 2160)
  link_NAG-ASN         : bond        0.00367 (    2)
  link_NAG-ASN         : angle       1.41552 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 TRP cc_start: 0.8113 (t-100) cc_final: 0.7873 (m-90)
REVERT: C  352 PHE cc_start: 0.6627 (m-10) cc_final: 0.5937 (t80)
REVERT: C  452 SER cc_start: 0.9134 (t) cc_final: 0.8700 (p)
REVERT: C  455 TYR cc_start: 0.7254 (m-80) cc_final: 0.6709 (m-80)
REVERT: A   37 MET cc_start: 0.8048 (ttm) cc_final: 0.7645 (ttp)
REVERT: A  193 TRP cc_start: 0.8196 (t-100) cc_final: 0.7947 (m-90)
REVERT: A  338 MET cc_start: 0.8531 (mtt) cc_final: 0.8200 (mtm)
REVERT: A  352 PHE cc_start: 0.6608 (m-10) cc_final: 0.5919 (t80)
REVERT: A  452 SER cc_start: 0.9115 (t) cc_final: 0.8750 (p)
REVERT: A  696 CYS cc_start: 0.7775 (m) cc_final: 0.7516 (t)
  outliers start: 34
  outliers final: 9
  residues processed: 112
  average time/residue: 0.3781
  time to fit residues: 46.6258
Evaluate side-chains
  88 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  673 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  673 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.130707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.094646 restraints weight = 17246.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.33
r_work: 0.3331 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.7542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9096  Z= 0.152
  Angle     :  0.581   8.669  12362  Z= 0.291
  Chirality :  0.042   0.299   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.275  27.379   1222
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  :  9.76 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.25), residues: 1110
  helix:  2.16 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.71 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 235 
 TYR   0.018   0.001   TYR C 451 
 PHE   0.023   0.001   PHE C 221 
 TRP   0.008   0.001   TRP C 460 
 HIS   0.004   0.001   HIS C 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9094)
  covalent geometry    : angle       0.58084 (12356)
  hydrogen bonds       : bond        0.04541 (  732)
  hydrogen bonds       : angle       4.51963 ( 2160)
  link_NAG-ASN         : bond        0.00370 (    2)
  link_NAG-ASN         : angle       1.32280 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 TRP cc_start: 0.8119 (t-100) cc_final: 0.7874 (m-90)
REVERT: C  352 PHE cc_start: 0.6662 (m-10) cc_final: 0.5960 (t80)
REVERT: C  402 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6579 (tt)
REVERT: C  452 SER cc_start: 0.9118 (t) cc_final: 0.8772 (p)
REVERT: C  521 MET cc_start: 0.5686 (mmt) cc_final: 0.5315 (mmm)
REVERT: C  667 ILE cc_start: 0.8376 (mm) cc_final: 0.8108 (pt)
REVERT: A   37 MET cc_start: 0.8130 (ttm) cc_final: 0.7690 (ttm)
REVERT: A  193 TRP cc_start: 0.8168 (t-100) cc_final: 0.7933 (m-90)
REVERT: A  352 PHE cc_start: 0.6664 (m-10) cc_final: 0.5970 (t80)
REVERT: A  402 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6608 (tt)
REVERT: A  452 SER cc_start: 0.9107 (t) cc_final: 0.8683 (p)
REVERT: A  696 CYS cc_start: 0.7844 (m) cc_final: 0.7531 (t)
  outliers start: 28
  outliers final: 11
  residues processed: 106
  average time/residue: 0.4262
  time to fit residues: 49.5036
Evaluate side-chains
  101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  673 LEU
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  673 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 109 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0570
   chunk 92 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.130801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.094756 restraints weight = 17180.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.31
r_work: 0.3330 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.7735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9096  Z= 0.150
  Angle     :  0.594  10.878  12362  Z= 0.293
  Chirality :  0.042   0.320   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.234  26.307   1222
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 10.98 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.85 (0.25), residues: 1110
  helix:  2.20 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.68 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 235 
 TYR   0.016   0.001   TYR A 451 
 PHE   0.021   0.001   PHE C 221 
 TRP   0.008   0.001   TRP A 460 
 HIS   0.004   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9094)
  covalent geometry    : angle       0.59351 (12356)
  hydrogen bonds       : bond        0.04508 (  732)
  hydrogen bonds       : angle       4.51431 ( 2160)
  link_NAG-ASN         : bond        0.00349 (    2)
  link_NAG-ASN         : angle       1.33587 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 TRP cc_start: 0.8107 (t-100) cc_final: 0.7877 (m-90)
REVERT: C  234 ASP cc_start: 0.8299 (m-30) cc_final: 0.7755 (t0)
REVERT: C  352 PHE cc_start: 0.6685 (m-10) cc_final: 0.5963 (t80)
REVERT: C  402 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6566 (tt)
REVERT: C  452 SER cc_start: 0.9088 (t) cc_final: 0.8663 (p)
REVERT: C  455 TYR cc_start: 0.7316 (m-80) cc_final: 0.6537 (m-80)
REVERT: C  521 MET cc_start: 0.5555 (mmt) cc_final: 0.5192 (mmm)
REVERT: C  667 ILE cc_start: 0.8321 (mm) cc_final: 0.8051 (pt)
REVERT: A   37 MET cc_start: 0.8135 (ttm) cc_final: 0.7695 (ttm)
REVERT: A  193 TRP cc_start: 0.8168 (t-100) cc_final: 0.7938 (m-90)
REVERT: A  234 ASP cc_start: 0.8269 (m-30) cc_final: 0.7750 (t0)
REVERT: A  352 PHE cc_start: 0.6634 (m-10) cc_final: 0.5926 (t80)
REVERT: A  402 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6454 (tt)
REVERT: A  452 SER cc_start: 0.9093 (t) cc_final: 0.8710 (p)
REVERT: A  667 ILE cc_start: 0.8335 (mt) cc_final: 0.8129 (mm)
  outliers start: 23
  outliers final: 7
  residues processed: 106
  average time/residue: 0.4385
  time to fit residues: 50.9312
Evaluate side-chains
  90 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  673 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  430 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 79 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0000
   chunk 73 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.131709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.096007 restraints weight = 17118.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.31
r_work: 0.3356 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.7916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9096  Z= 0.137
  Angle     :  0.590  12.386  12362  Z= 0.288
  Chirality :  0.041   0.329   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.171  25.670   1222
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.59 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.85 (0.25), residues: 1110
  helix:  2.19 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop :  0.63 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 235 
 TYR   0.016   0.001   TYR C 451 
 PHE   0.019   0.001   PHE C 221 
 TRP   0.008   0.001   TRP C 460 
 HIS   0.004   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9094)
  covalent geometry    : angle       0.58917 (12356)
  hydrogen bonds       : bond        0.04381 (  732)
  hydrogen bonds       : angle       4.46095 ( 2160)
  link_NAG-ASN         : bond        0.00351 (    2)
  link_NAG-ASN         : angle       1.35268 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: C  352 PHE cc_start: 0.6644 (m-10) cc_final: 0.5962 (t80)
REVERT: C  402 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6521 (tt)
REVERT: C  452 SER cc_start: 0.9104 (t) cc_final: 0.8675 (p)
REVERT: C  455 TYR cc_start: 0.7438 (m-80) cc_final: 0.6779 (m-80)
REVERT: C  519 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7077 (mp0)
REVERT: C  521 MET cc_start: 0.5529 (mmt) cc_final: 0.5215 (mmm)
REVERT: C  667 ILE cc_start: 0.8320 (mm) cc_final: 0.8072 (pt)
REVERT: A   37 MET cc_start: 0.8123 (ttm) cc_final: 0.7658 (ttp)
REVERT: A  352 PHE cc_start: 0.6665 (m-10) cc_final: 0.5963 (t80)
REVERT: A  402 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6455 (tt)
REVERT: A  452 SER cc_start: 0.9095 (t) cc_final: 0.8659 (p)
REVERT: A  455 TYR cc_start: 0.7361 (m-80) cc_final: 0.6562 (m-80)
  outliers start: 17
  outliers final: 5
  residues processed: 97
  average time/residue: 0.4684
  time to fit residues: 49.4193
Evaluate side-chains
  91 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  673 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 84 optimal weight:    0.1980
   chunk 56 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.131225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.095476 restraints weight = 17048.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.29
r_work: 0.3359 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.8126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9096  Z= 0.147
  Angle     :  0.603  10.735  12362  Z= 0.293
  Chirality :  0.042   0.323   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.152  24.419   1222
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.60 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.25), residues: 1110
  helix:  2.20 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.65 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  61 
 TYR   0.023   0.001   TYR A 407 
 PHE   0.020   0.001   PHE A 221 
 TRP   0.008   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9094)
  covalent geometry    : angle       0.60232 (12356)
  hydrogen bonds       : bond        0.04449 (  732)
  hydrogen bonds       : angle       4.44426 ( 2160)
  link_NAG-ASN         : bond        0.00322 (    2)
  link_NAG-ASN         : angle       1.32377 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  234 ASP cc_start: 0.8348 (m-30) cc_final: 0.7790 (t0)
REVERT: C  352 PHE cc_start: 0.6715 (m-10) cc_final: 0.5992 (t80)
REVERT: C  402 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6459 (tt)
REVERT: C  409 GLN cc_start: 0.8510 (tp40) cc_final: 0.8177 (tt0)
REVERT: C  452 SER cc_start: 0.9139 (t) cc_final: 0.8720 (p)
REVERT: C  455 TYR cc_start: 0.7383 (m-80) cc_final: 0.6848 (m-80)
REVERT: C  519 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7044 (mp0)
REVERT: C  521 MET cc_start: 0.5479 (mmt) cc_final: 0.5179 (mmm)
REVERT: A   37 MET cc_start: 0.8125 (ttm) cc_final: 0.7692 (ttm)
REVERT: A  234 ASP cc_start: 0.8319 (m-30) cc_final: 0.7823 (t0)
REVERT: A  352 PHE cc_start: 0.6722 (m-10) cc_final: 0.5987 (t80)
REVERT: A  452 SER cc_start: 0.9109 (t) cc_final: 0.8665 (p)
REVERT: A  455 TYR cc_start: 0.7391 (m-80) cc_final: 0.6543 (m-80)
  outliers start: 14
  outliers final: 6
  residues processed: 101
  average time/residue: 0.4890
  time to fit residues: 53.6558
Evaluate side-chains
  87 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  673 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.130245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.094404 restraints weight = 17080.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.29
r_work: 0.3324 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.8309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9096  Z= 0.160
  Angle     :  0.614  11.296  12362  Z= 0.298
  Chirality :  0.042   0.330   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.151  22.451   1222
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.60 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.80 (0.25), residues: 1110
  helix:  2.15 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.68 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 295 
 TYR   0.017   0.001   TYR A 451 
 PHE   0.022   0.002   PHE C 221 
 TRP   0.007   0.001   TRP C 460 
 HIS   0.004   0.001   HIS C 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9094)
  covalent geometry    : angle       0.61302 (12356)
  hydrogen bonds       : bond        0.04535 (  732)
  hydrogen bonds       : angle       4.49113 ( 2160)
  link_NAG-ASN         : bond        0.00311 (    2)
  link_NAG-ASN         : angle       1.32161 (    6)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.342 
Fit side-chains
REVERT: C  211 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8738 (mm)
REVERT: C  352 PHE cc_start: 0.6720 (m-10) cc_final: 0.5977 (t80)
REVERT: C  402 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6604 (tt)
REVERT: C  409 GLN cc_start: 0.8536 (tp40) cc_final: 0.8330 (tt0)
REVERT: C  452 SER cc_start: 0.9140 (t) cc_final: 0.8696 (p)
REVERT: C  455 TYR cc_start: 0.7350 (m-80) cc_final: 0.6801 (m-80)
REVERT: C  521 MET cc_start: 0.5372 (mmt) cc_final: 0.5140 (mmm)
REVERT: A  211 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: A  352 PHE cc_start: 0.6712 (m-10) cc_final: 0.5981 (t80)
REVERT: A  452 SER cc_start: 0.9104 (t) cc_final: 0.8660 (p)
REVERT: A  455 TYR cc_start: 0.7289 (m-80) cc_final: 0.6637 (m-80)
  outliers start: 15
  outliers final: 6
  residues processed: 89
  average time/residue: 0.4902
  time to fit residues: 47.3994
Evaluate side-chains
  92 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 106 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.130324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.094448 restraints weight = 16858.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.28
r_work: 0.3325 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.8405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9096  Z= 0.162
  Angle     :  0.636  12.725  12362  Z= 0.305
  Chirality :  0.042   0.331   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.146  21.240   1222
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 13.31 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.25), residues: 1110
  helix:  2.10 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop :  0.63 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  41 
 TYR   0.022   0.002   TYR C 407 
 PHE   0.021   0.001   PHE C 221 
 TRP   0.007   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 9094)
  covalent geometry    : angle       0.63517 (12356)
  hydrogen bonds       : bond        0.04515 (  732)
  hydrogen bonds       : angle       4.49807 ( 2160)
  link_NAG-ASN         : bond        0.00317 (    2)
  link_NAG-ASN         : angle       1.32270 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3743.62 seconds
wall clock time: 64 minutes 36.67 seconds (3876.67 seconds total)