Starting phenix.real_space_refine
on Thu Feb 13 10:05:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u58_41914/02_2025/8u58_41914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u58_41914/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u58_41914/02_2025/8u58_41914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u58_41914/02_2025/8u58_41914.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u58_41914/02_2025/8u58_41914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u58_41914/02_2025/8u58_41914.cif"
  }
  resolution = 2.45
  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=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8884
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      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: "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
  Restraints were copied for chains:
    C
  Time building chain proxies: 8.11, per 1000 atoms: 0.91
  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: 2.15
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.93
  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: 3.06

  Time building geometry restraints manager: 2.50 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.940
  Find NCS groups from input model:        0.150
  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:12.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.490
-------------------------------------------------------------------------------
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   9094  Z= 0.467
  Angle     :  1.056   9.462  12356  Z= 0.603
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (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
 TRP   0.031   0.006   TRP A 100 
 HIS   0.007   0.003   HIS A 505 
 PHE   0.054   0.007   PHE A 694 
 TYR   0.096   0.009   TYR A 320 
 ARG   0.004   0.001   ARG A 687 

*********************** 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  : 1.041 
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: 1.0253
  time to fit residues: 223.6849
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  : 0.969 
-------------------------------------------------------------------------------
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 94 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 87 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   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 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 654 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.133105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.098217 restraints weight = 16604.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.25
r_work: 0.3374 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9094  Z= 0.278
  Angle     :  0.692   8.469  12356  Z= 0.355
  Chirality :  0.046   0.173   1502
  Planarity :  0.005   0.034   1476
  Dihedral  :  4.933  34.849   1224
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 10.16 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.88 (0.25), residues: 1110
  helix:  1.51 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.40 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 396 
 HIS   0.004   0.001   HIS A 310 
 PHE   0.022   0.002   PHE C 221 
 TYR   0.028   0.002   TYR C 455 
 ARG   0.006   0.001   ARG A 295 

*********************** 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
  141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: C  112 SER cc_start: 0.8986 (m) cc_final: 0.8723 (t)
REVERT: C  130 ARG cc_start: 0.7702 (ptt180) cc_final: 0.7499 (ptp90)
REVERT: C  242 GLU cc_start: 0.8274 (tp30) cc_final: 0.8035 (tp30)
REVERT: C  382 VAL cc_start: 0.8020 (t) cc_final: 0.7789 (t)
REVERT: A   37 MET cc_start: 0.7539 (ttm) cc_final: 0.7217 (ttm)
REVERT: A  112 SER cc_start: 0.9018 (m) cc_final: 0.8775 (t)
REVERT: A  193 TRP cc_start: 0.8145 (t-100) cc_final: 0.7704 (t-100)
REVERT: A  242 GLU cc_start: 0.8305 (tp30) cc_final: 0.8057 (tp30)
REVERT: A  382 VAL cc_start: 0.8047 (t) cc_final: 0.7835 (t)
REVERT: A  540 MET cc_start: 0.6282 (mmm) cc_final: 0.5981 (tmt)
  outliers start: 26
  outliers final: 3
  residues processed: 132
  average time/residue: 0.8991
  time to fit residues: 130.0879
Evaluate side-chains
  84 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  239 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 107 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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
A 658 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.131368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.095069 restraints weight = 16908.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.31
r_work: 0.3342 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.6147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9094  Z= 0.253
  Angle     :  0.645  11.349  12356  Z= 0.322
  Chirality :  0.042   0.154   1502
  Planarity :  0.004   0.037   1476
  Dihedral  :  4.615  30.559   1222
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.16 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.45 (0.25), residues: 1110
  helix:  1.88 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.73 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 193 
 HIS   0.003   0.001   HIS C 716 
 PHE   0.025   0.002   PHE C 221 
 TYR   0.033   0.002   TYR C 455 
 ARG   0.006   0.001   ARG C 235 

*********************** 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: 27
    poor density    : 98
  time to evaluate  : 1.010 
Fit side-chains
REVERT: C  145 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8966 (t0)
REVERT: C  234 ASP cc_start: 0.8008 (m-30) cc_final: 0.7295 (t0)
REVERT: C  338 MET cc_start: 0.8520 (mtt) cc_final: 0.8185 (mtm)
REVERT: C  352 PHE cc_start: 0.6814 (m-10) cc_final: 0.6273 (t80)
REVERT: C  401 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7479 (tp)
REVERT: C  452 SER cc_start: 0.9038 (t) cc_final: 0.8608 (p)
REVERT: C  519 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6960 (mp0)
REVERT: C  540 MET cc_start: 0.6330 (mmm) cc_final: 0.5996 (tmt)
REVERT: A   37 MET cc_start: 0.7909 (ttm) cc_final: 0.7499 (ttp)
REVERT: A  193 TRP cc_start: 0.8225 (t-100) cc_final: 0.7925 (m-90)
REVERT: A  234 ASP cc_start: 0.8009 (m-30) cc_final: 0.7310 (t0)
REVERT: A  299 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8125 (mt-10)
REVERT: A  338 MET cc_start: 0.8448 (mtt) cc_final: 0.8113 (mtm)
REVERT: A  352 PHE cc_start: 0.6845 (m-10) cc_final: 0.6277 (t80)
REVERT: A  401 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7483 (tp)
REVERT: A  519 GLU cc_start: 0.7795 (mm-30) cc_final: 0.6891 (mp0)
REVERT: A  540 MET cc_start: 0.6389 (mmm) cc_final: 0.6178 (tmt)
  outliers start: 27
  outliers final: 7
  residues processed: 119
  average time/residue: 0.9991
  time to fit residues: 129.1557
Evaluate side-chains
  82 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
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  389 VAL
Chi-restraints excluded: chain C residue  395 ILE
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  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 11 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   chunk 97 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8180

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.131166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.094943 restraints weight = 17038.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.31
r_work: 0.3337 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.6804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9094  Z= 0.237
  Angle     :  0.611  13.109  12356  Z= 0.303
  Chirality :  0.042   0.387   1502
  Planarity :  0.004   0.034   1476
  Dihedral  :  4.420  29.777   1222
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.67 %
    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 (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:  2.67 (0.25), residues: 1110
  helix:  2.05 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.68 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 396 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.023   0.002   PHE A 221 
 TYR   0.019   0.001   TYR C 455 
 ARG   0.003   0.000   ARG A 295 

*********************** 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
  104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.959 
Fit side-chains
REVERT: C   37 MET cc_start: 0.7963 (ttm) cc_final: 0.7562 (ttm)
REVERT: C  338 MET cc_start: 0.8490 (mtt) cc_final: 0.8147 (mtm)
REVERT: C  352 PHE cc_start: 0.6716 (m-10) cc_final: 0.6028 (t80)
REVERT: C  401 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7494 (mp)
REVERT: C  402 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6712 (tt)
REVERT: C  452 SER cc_start: 0.8989 (t) cc_final: 0.8588 (p)
REVERT: C  521 MET cc_start: 0.5666 (tpt) cc_final: 0.5224 (mmm)
REVERT: C  540 MET cc_start: 0.6583 (mmm) cc_final: 0.6154 (tmt)
REVERT: A   37 MET cc_start: 0.8034 (ttm) cc_final: 0.7579 (ttm)
REVERT: A  193 TRP cc_start: 0.8212 (t-100) cc_final: 0.7908 (m-90)
REVERT: A  338 MET cc_start: 0.8513 (mtt) cc_final: 0.8153 (mtm)
REVERT: A  352 PHE cc_start: 0.6710 (m-10) cc_final: 0.6012 (t80)
REVERT: A  401 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7474 (tp)
REVERT: A  402 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6686 (tt)
  outliers start: 25
  outliers final: 8
  residues processed: 99
  average time/residue: 0.8839
  time to fit residues: 96.4779
Evaluate side-chains
  89 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  307 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
Chi-restraints excluded: chain A residue  402 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.130664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.094787 restraints weight = 17054.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.31
r_work: 0.3333 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.7250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9094  Z= 0.220
  Angle     :  0.587   8.610  12356  Z= 0.291
  Chirality :  0.043   0.325   1502
  Planarity :  0.004   0.034   1476
  Dihedral  :  4.350  28.437   1222
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  :  9.65 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.76 (0.25), residues: 1110
  helix:  2.13 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.66 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 363 
 HIS   0.004   0.001   HIS C 716 
 PHE   0.023   0.002   PHE A 221 
 TYR   0.018   0.002   TYR C 455 
 ARG   0.002   0.000   ARG C 235 

*********************** 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: 33
    poor density    : 85
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 MET cc_start: 0.8517 (mtt) cc_final: 0.8187 (mtm)
REVERT: C  352 PHE cc_start: 0.6669 (m-10) cc_final: 0.5978 (t80)
REVERT: C  401 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7564 (mp)
REVERT: C  402 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6595 (tt)
REVERT: C  452 SER cc_start: 0.9009 (t) cc_final: 0.8625 (p)
REVERT: C  519 GLU cc_start: 0.7836 (mm-30) cc_final: 0.6998 (mp0)
REVERT: C  521 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5109 (mmm)
REVERT: C  540 MET cc_start: 0.6633 (mmm) cc_final: 0.6424 (ptp)
REVERT: A  193 TRP cc_start: 0.8188 (t-100) cc_final: 0.7912 (m-90)
REVERT: A  338 MET cc_start: 0.8516 (mtt) cc_final: 0.8168 (mtm)
REVERT: A  352 PHE cc_start: 0.6633 (m-10) cc_final: 0.5945 (t80)
REVERT: A  402 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6642 (tt)
REVERT: A  452 SER cc_start: 0.9022 (t) cc_final: 0.8641 (p)
  outliers start: 33
  outliers final: 11
  residues processed: 108
  average time/residue: 0.9503
  time to fit residues: 112.2051
Evaluate side-chains
  99 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
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  389 VAL
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  521 MET
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  307 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  402 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 46 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 106 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.130441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.094502 restraints weight = 17116.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.32
r_work: 0.3324 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.7612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9094  Z= 0.222
  Angle     :  0.591   9.028  12356  Z= 0.294
  Chirality :  0.043   0.336   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.278  27.047   1222
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  :  9.45 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.80 (0.25), residues: 1110
  helix:  2.16 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.65 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 460 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.024   0.002   PHE C 221 
 TYR   0.044   0.002   TYR C 455 
 ARG   0.001   0.000   ARG C 235 

*********************** 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
  120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 88
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 MET cc_start: 0.8515 (mtt) cc_final: 0.8225 (mtp)
REVERT: C  352 PHE cc_start: 0.6717 (m-10) cc_final: 0.5980 (t80)
REVERT: C  402 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6524 (tt)
REVERT: C  452 SER cc_start: 0.9067 (t) cc_final: 0.8614 (p)
REVERT: C  521 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.5043 (mmm)
REVERT: C  667 ILE cc_start: 0.8272 (mp) cc_final: 0.8060 (pt)
REVERT: A  193 TRP cc_start: 0.8181 (t-100) cc_final: 0.7921 (m-90)
REVERT: A  234 ASP cc_start: 0.8292 (m-30) cc_final: 0.7691 (t0)
REVERT: A  338 MET cc_start: 0.8490 (mtt) cc_final: 0.8177 (mtm)
REVERT: A  352 PHE cc_start: 0.6670 (m-10) cc_final: 0.5949 (t80)
REVERT: A  402 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6597 (tt)
REVERT: A  452 SER cc_start: 0.9050 (t) cc_final: 0.8589 (p)
REVERT: A  455 TYR cc_start: 0.7314 (m-80) cc_final: 0.6569 (m-80)
  outliers start: 32
  outliers final: 12
  residues processed: 108
  average time/residue: 0.8794
  time to fit residues: 104.7697
Evaluate side-chains
  99 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
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  389 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  308 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 88 optimal weight:    0.5980
   chunk 96 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 99 optimal weight:    9.9990
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.130246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.094289 restraints weight = 17106.741|
|-----------------------------------------------------------------------------|
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: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.7856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9094  Z= 0.221
  Angle     :  0.588  10.645  12356  Z= 0.292
  Chirality :  0.042   0.338   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.260  25.624   1222
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.47 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.79 (0.25), residues: 1110
  helix:  2.14 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.70 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 460 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.022   0.002   PHE C 221 
 TYR   0.017   0.001   TYR A 451 
 ARG   0.001   0.000   ARG C 295 

*********************** 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
  111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  234 ASP cc_start: 0.8341 (m-30) cc_final: 0.7822 (t0)
REVERT: C  297 MET cc_start: 0.8715 (mmt) cc_final: 0.8440 (mmt)
REVERT: C  352 PHE cc_start: 0.6769 (m-10) cc_final: 0.6028 (t80)
REVERT: C  452 SER cc_start: 0.9128 (t) cc_final: 0.8702 (p)
REVERT: C  455 TYR cc_start: 0.7551 (m-80) cc_final: 0.6581 (m-80)
REVERT: C  521 MET cc_start: 0.5388 (OUTLIER) cc_final: 0.4621 (mmm)
REVERT: C  667 ILE cc_start: 0.8245 (mp) cc_final: 0.8029 (pt)
REVERT: A  193 TRP cc_start: 0.8167 (t-100) cc_final: 0.7957 (m-90)
REVERT: A  352 PHE cc_start: 0.6720 (m-10) cc_final: 0.5983 (t80)
REVERT: A  402 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6689 (tt)
REVERT: A  452 SER cc_start: 0.9071 (t) cc_final: 0.8717 (p)
REVERT: A  667 ILE cc_start: 0.8343 (mt) cc_final: 0.8131 (mm)
  outliers start: 25
  outliers final: 10
  residues processed: 105
  average time/residue: 0.8874
  time to fit residues: 102.4610
Evaluate side-chains
  92 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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  389 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 96 optimal weight:    8.9990
   chunk 94 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
** A 145 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 = 0.4062 r_free = 0.4062 target = 0.130224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.094393 restraints weight = 17307.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.30
r_work: 0.3326 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.8044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9094  Z= 0.216
  Angle     :  0.601  11.291  12356  Z= 0.296
  Chirality :  0.042   0.338   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.208  24.523   1222
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 11.38 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.81 (0.25), residues: 1110
  helix:  2.15 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.70 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.021   0.001   PHE C 221 
 TYR   0.015   0.001   TYR C 451 
 ARG   0.001   0.000   ARG C 130 

*********************** 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
  106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: C  297 MET cc_start: 0.8723 (mmt) cc_final: 0.8450 (mmt)
REVERT: C  352 PHE cc_start: 0.6758 (m-10) cc_final: 0.6020 (t80)
REVERT: C  409 GLN cc_start: 0.8501 (tp40) cc_final: 0.8112 (tt0)
REVERT: C  452 SER cc_start: 0.9100 (t) cc_final: 0.8708 (p)
REVERT: C  521 MET cc_start: 0.5341 (OUTLIER) cc_final: 0.4604 (mmm)
REVERT: A  234 ASP cc_start: 0.8342 (m-30) cc_final: 0.7821 (t0)
REVERT: A  352 PHE cc_start: 0.6689 (m-10) cc_final: 0.5939 (t80)
REVERT: A  402 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6617 (tt)
REVERT: A  452 SER cc_start: 0.9117 (t) cc_final: 0.8722 (p)
  outliers start: 21
  outliers final: 7
  residues processed: 100
  average time/residue: 0.9751
  time to fit residues: 106.7921
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  : 0.994 
-------------------------------------------------------------------------------
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  419 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain A residue  307 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0000
   chunk 80 optimal weight:    0.6980
   chunk 108 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.6384

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.130911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.095268 restraints weight = 17150.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.30
r_work: 0.3339 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.8221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9094  Z= 0.206
  Angle     :  0.622  12.835  12356  Z= 0.300
  Chirality :  0.042   0.342   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.172  23.597   1222
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.40 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.84 (0.25), residues: 1110
  helix:  2.19 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.66 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 460 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.020   0.001   PHE A 221 
 TYR   0.021   0.001   TYR A 407 
 ARG   0.001   0.000   ARG A 235 

*********************** 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
  98 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 1.026 
Fit side-chains
REVERT: C  234 ASP cc_start: 0.8302 (m-30) cc_final: 0.7835 (t0)
REVERT: C  297 MET cc_start: 0.8715 (mmt) cc_final: 0.8446 (mmt)
REVERT: C  352 PHE cc_start: 0.6701 (m-10) cc_final: 0.6033 (t80)
REVERT: C  409 GLN cc_start: 0.8534 (tp40) cc_final: 0.8311 (tt0)
REVERT: C  452 SER cc_start: 0.9120 (t) cc_final: 0.8682 (p)
REVERT: C  455 TYR cc_start: 0.7431 (m-80) cc_final: 0.6562 (m-80)
REVERT: C  521 MET cc_start: 0.5362 (OUTLIER) cc_final: 0.4831 (mmm)
REVERT: A  352 PHE cc_start: 0.6710 (m-10) cc_final: 0.6011 (t80)
REVERT: A  402 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6514 (tt)
REVERT: A  452 SER cc_start: 0.9158 (t) cc_final: 0.8771 (p)
REVERT: A  667 ILE cc_start: 0.8322 (mt) cc_final: 0.8097 (mm)
  outliers start: 14
  outliers final: 7
  residues processed: 93
  average time/residue: 1.0119
  time to fit residues: 102.6280
Evaluate side-chains
  86 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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  419 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  308 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 40 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 102 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 4 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:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.130680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.095149 restraints weight = 17144.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.30
r_work: 0.3340 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.8360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9094  Z= 0.213
  Angle     :  0.626  11.653  12356  Z= 0.303
  Chirality :  0.042   0.339   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.169  22.530   1222
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.70 %
    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 (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:  2.80 (0.25), residues: 1110
  helix:  2.16 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.62 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.019   0.001   PHE C 221 
 TYR   0.021   0.002   TYR C 407 
 ARG   0.001   0.000   ARG C 235 

********************** 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: 14
    poor density    : 79
  time to evaluate  : 1.024 
Fit side-chains
REVERT: C  297 MET cc_start: 0.8718 (mmt) cc_final: 0.8462 (mmt)
REVERT: C  352 PHE cc_start: 0.6744 (m-10) cc_final: 0.6013 (t80)
REVERT: C  409 GLN cc_start: 0.8597 (tp40) cc_final: 0.8369 (tt0)
REVERT: C  452 SER cc_start: 0.9120 (t) cc_final: 0.8693 (p)
REVERT: C  521 MET cc_start: 0.5307 (OUTLIER) cc_final: 0.4787 (mmm)
REVERT: A  211 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8750 (mm)
REVERT: A  234 ASP cc_start: 0.8286 (m-30) cc_final: 0.7833 (t0)
REVERT: A  352 PHE cc_start: 0.6744 (m-10) cc_final: 0.6019 (t80)
REVERT: A  402 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6514 (tt)
REVERT: A  452 SER cc_start: 0.9132 (t) cc_final: 0.8722 (p)
  outliers start: 14
  outliers final: 6
  residues processed: 87
  average time/residue: 0.9751
  time to fit residues: 92.7204
Evaluate side-chains
  86 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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  419 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  308 VAL
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 54 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 72 optimal weight:    0.4980
   chunk 50 optimal weight:    8.9990
   chunk 74 optimal weight:    1.9990
   chunk 99 optimal weight:   20.0000
   chunk 79 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 96 optimal weight:    7.9990
   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 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.130453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.094889 restraints weight = 17056.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.30
r_work: 0.3334 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.8468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9094  Z= 0.221
  Angle     :  0.639  11.417  12356  Z= 0.306
  Chirality :  0.042   0.343   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.150  21.259   1222
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.60 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.81 (0.25), residues: 1110
  helix:  2.16 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.66 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 460 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.021   0.001   PHE C 221 
 TYR   0.015   0.001   TYR C 455 
 ARG   0.001   0.000   ARG C 235 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6997.47 seconds
wall clock time: 124 minutes 6.79 seconds (7446.79 seconds total)