Starting phenix.real_space_refine
on Sat May  2 13:30:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11oo_75889/05_2026/11oo_75889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11oo_75889/05_2026/11oo_75889.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/11oo_75889/05_2026/11oo_75889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11oo_75889/05_2026/11oo_75889.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/11oo_75889/05_2026/11oo_75889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11oo_75889/05_2026/11oo_75889.cif"
  }
  resolution = 3.4
  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=  -0.000 sd=   0.007
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      24      5.16       5
     C    3643      2.51       5
     N     987      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5778
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1650
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 1583
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 197, 1572
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 197, 1572
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 1607
    Chain: "K"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "H"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1606
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199}
          Chain breaks: 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
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASN A 450 " occ=0.14
      ... (14 atoms not shown)
      pdb=" ND2BASN A 450 " occ=0.86
  Time building chain proxies: 1.80, per 1000 atoms: 0.31
  Number of scatterers: 5778
  At special positions: 0
  Unit cell: (76.752, 77.688, 124.488, 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      24     16.00
     O    1124      8.00
     N     987      7.00
     C    3643      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 216 " - pdb=" SG  CYS H 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " distance=2.03

  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 601 " - " ASN A 343 "
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 389.3 milliseconds
  

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1372

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 17 sheets defined
      10.5% alpha, 40.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'L' and resid 123 through 128
      removed outlier: 3.501A  pdb=" N   LYS L 128 " --> pdb=" O   ASP L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 190
      removed outlier: 3.635A  pdb=" N   LYS L 190 " --> pdb=" O   ALA L 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.612A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 386 through 390
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 4.338A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'K' and resid 87 through 91
      removed outlier: 3.967A  pdb=" N   THR K  91 " --> pdb=" O   PRO K  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.503A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.785A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 159 through 161
      No H-bonds generated for 'chain 'H' and resid 159 through 161'
    Processing helix  chain 'H' and resid 190 through 194
      removed outlier: 3.750A  pdb=" N   GLY H 193 " --> pdb=" O   SER H 190 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.632A  pdb=" N   ASP L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.768A  pdb=" N   VAL L  86 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.522A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 116 through 120
      removed outlier: 3.527A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 155 through 157
      removed outlier: 4.667A  pdb=" N   TRP L 150 " --> pdb=" O   GLN L 157 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR L 194 " --> pdb=" O   PHE L 211 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA9, first strand: chain 'K' and resid 5 through 6
    Processing sheet with id=AB1, first strand: chain 'K' and resid 58 through 60
      removed outlier: 5.266A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   TYR K 110 " --> pdb=" O   ILE K  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 58 through 60
      removed outlier: 5.266A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   THR K 115 " --> pdb=" O   TYR K  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.712A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  81 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.919A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.487A  pdb=" N   GLY H  33 " --> pdb=" O   ASP H  99 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 123 through 127
      removed outlier: 3.963A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 123 through 127
      removed outlier: 3.963A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 154 through 157
      removed outlier: 4.761A  pdb=" N   TYR H 197 " --> pdb=" O   VAL H 214 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   CYS H 199 " --> pdb=" O   LYS H 212 " (cutoff:3.500A)

    237 hydrogen bonds defined for protein.
    576 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: 1.07

  Time building geometry restraints manager: 0.57 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: 1864
        1.34 -     1.46: 1243
        1.46 -     1.57: 2788
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 5923
  Sorted by residual:
  bond pdb=" C   ALA A 372 "
       pdb=" N   PRO A 373 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.42e+00
  bond pdb=" CB  GLU L 125 "
       pdb=" CG  GLU L 125 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.19e+00
  bond pdb=" CA  VAL H  50 "
       pdb=" CB  VAL H  50 "
    ideal  model  delta    sigma   weight residual
    1.550  1.540  0.010 1.03e-02 9.43e+03 1.00e+00
  bond pdb=" CB  ARG K  31 "
       pdb=" CG  ARG K  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.39e-01
  bond pdb=" CB  GLN H 108 "
       pdb=" CG  GLN H 108 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.22e-01
  ... (remaining 5918 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 7651
        1.25 -     2.49: 314
        2.49 -     3.74: 69
        3.74 -     4.99: 14
        4.99 -     6.23: 6
  Bond angle restraints: 8054
  Sorted by residual:
  angle pdb=" C   PHE A 371 "
        pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
      ideal   model   delta    sigma   weight residual
     120.09  124.70   -4.61 1.25e+00 6.40e-01 1.36e+01
  angle pdb=" CA  ARG K  31 "
        pdb=" CB  ARG K  31 "
        pdb=" CG  ARG K  31 "
      ideal   model   delta    sigma   weight residual
     114.10  120.33   -6.23 2.00e+00 2.50e-01 9.71e+00
  angle pdb=" CB  GLU L 125 "
        pdb=" CG  GLU L 125 "
        pdb=" CD  GLU L 125 "
      ideal   model   delta    sigma   weight residual
     112.60  116.94   -4.34 1.70e+00 3.46e-01 6.51e+00
  angle pdb=" C   GLY A 476 "
        pdb=" N   ASN A 477 "
        pdb=" CA  ASN A 477 "
      ideal   model   delta    sigma   weight residual
     121.54  126.24   -4.70 1.91e+00 2.74e-01 6.06e+00
  angle pdb=" N   PRO A 499 "
        pdb=" CA  PRO A 499 "
        pdb=" C   PRO A 499 "
      ideal   model   delta    sigma   weight residual
     114.92  112.11    2.81 1.19e+00 7.06e-01 5.56e+00
  ... (remaining 8049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 3180
       16.44 -    32.88: 260
       32.88 -    49.32: 69
       49.32 -    65.76: 11
       65.76 -    82.19: 13
  Dihedral angle restraints: 3533
    sinusoidal: 1372
      harmonic: 2161
  Sorted by residual:
  dihedral pdb=" CB  CYS L 216 "
           pdb=" SG  CYS L 216 "
           pdb=" SG  CYS H 219 "
           pdb=" CB  CYS H 219 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.81  -82.19     1      1.00e+01 1.00e-02 8.30e+01
  dihedral pdb=" CB  CYS K  22 "
           pdb=" SG  CYS K  22 "
           pdb=" SG  CYS K  96 "
           pdb=" CB  CYS K  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.70   37.30     1      1.00e+01 1.00e-02 1.96e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.16  -37.16     1      1.00e+01 1.00e-02 1.95e+01
  ... (remaining 3530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 602
       0.040 -    0.080: 186
       0.080 -    0.120: 74
       0.120 -    0.160: 11
       0.160 -    0.201: 1
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" CB  THR A 430 "
            pdb=" CA  THR A 430 "
            pdb=" OG1 THR A 430 "
            pdb=" CG2 THR A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CG  LEU K   4 "
            pdb=" CB  LEU K   4 "
            pdb=" CD1 LEU K   4 "
            pdb=" CD2 LEU K   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CA  ASN A 477 "
            pdb=" N   ASN A 477 "
            pdb=" C   ASN A 477 "
            pdb=" CB  ASN A 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.12e-01
  ... (remaining 871 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  95 "    0.047 5.00e-02 4.00e+02   7.06e-02 7.97e+00
        pdb=" N   PRO L  96 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO L  96 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO L  96 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU L  80 "   -0.043 5.00e-02 4.00e+02   6.49e-02 6.73e+00
        pdb=" N   PRO L  81 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "    0.039 5.00e-02 4.00e+02   5.90e-02 5.57e+00
        pdb=" N   PRO A 463 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 3175
        3.01 -     3.48: 5410
        3.48 -     3.96: 9085
        3.96 -     4.43: 10575
        4.43 -     4.90: 17638
  Nonbonded interactions: 45883
  Sorted by model distance:
  nonbonded pdb=" N   GLU L 125 "
            pdb=" OE1 GLU L 125 "
     model   vdw
     2.538 3.120
  nonbonded pdb=" N   GLN H 108 "
            pdb=" OE1 GLN H 108 "
     model   vdw
     2.562 3.120
  nonbonded pdb=" OD1 ASP A 420 "
            pdb=" OD1 ASN A 460 "
     model   vdw
     2.572 3.040
  nonbonded pdb=" O   GLY A 476 "
            pdb=" OD1 ASN A 477 "
     model   vdw
     2.572 3.040
  nonbonded pdb=" O   ASN A 343 "
            pdb=" OD1 ASN A 343 "
     model   vdw
     2.578 3.040
  ... (remaining 45878 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.09 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:             8.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.610
  Find NCS groups from input model:        0.030
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
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      :  0.004   0.033   5934  Z= 0.162
  Angle     :  0.627   6.234   8077  Z= 0.341
  Chirality :  0.045   0.201    874
  Planarity :  0.006   0.071   1047
  Dihedral  : 13.551  79.834   2131
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.03 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  0.16 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.63 (0.32), residues: 740
  helix: -3.06 (0.61), residues: 49
  sheet: -0.32 (0.30), residues: 295
  loop :  0.03 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 452 
 TYR   0.020   0.001   TYR A 351 
 PHE   0.010   0.001   PHE L  72 
 TRP   0.010   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 5923)
  covalent geometry    : angle       0.62577 ( 8054)
  SS BOND              : bond        0.00179 (   10)
  SS BOND              : angle       0.46901 (   20)
  hydrogen bonds       : bond        0.24616 (  198)
  hydrogen bonds       : angle      11.60092 (  576)
  link_NAG-ASN         : bond        0.00030 (    1)
  link_NAG-ASN         : angle       2.34411 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  382 VAL cc_start: 0.8593 (p) cc_final: 0.8361 (m)
REVERT: H   78 THR cc_start: 0.8949 (m) cc_final: 0.8462 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0939
  time to fit residues: 10.4139
Evaluate side-chains
  73 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
H 202 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.150214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.118923 restraints weight = 21024.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 6.02
r_work: 0.2919 rms_B_bonded: 5.92 restraints_weight: 2.0000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5934  Z= 0.214
  Angle     :  0.618   7.898   8077  Z= 0.327
  Chirality :  0.046   0.146    874
  Planarity :  0.006   0.063   1047
  Dihedral  :  4.808  52.305    847
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.76 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  7.13 %
    Favored  : 92.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.72 (0.31), residues: 740
  helix: -3.23 (0.62), residues: 50
  sheet: -0.31 (0.29), residues: 301
  loop : -0.07 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 452 
 TYR   0.017   0.001   TYR A 473 
 PHE   0.014   0.002   PHE A 400 
 TRP   0.012   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 5923)
  covalent geometry    : angle       0.61643 ( 8054)
  SS BOND              : bond        0.00273 (   10)
  SS BOND              : angle       0.59776 (   20)
  hydrogen bonds       : bond        0.03885 (  198)
  hydrogen bonds       : angle       7.43347 (  576)
  link_NAG-ASN         : bond        0.00169 (    1)
  link_NAG-ASN         : angle       2.15896 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8444 (tt0) cc_final: 0.8079 (tt0)
REVERT: A  382 VAL cc_start: 0.8964 (p) cc_final: 0.8740 (m)
REVERT: A  478 LYS cc_start: 0.7447 (mmtm) cc_final: 0.7244 (mmtm)
REVERT: H   56 SER cc_start: 0.7839 (m) cc_final: 0.7581 (p)
REVERT: H   78 THR cc_start: 0.9059 (m) cc_final: 0.8558 (p)
REVERT: H  202 ASN cc_start: 0.7904 (m-40) cc_final: 0.7480 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 80
  average time/residue: 0.0867
  time to fit residues: 8.8575
Evaluate side-chains
  77 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 66 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0060
   chunk 40 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.154559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.124164 restraints weight = 26968.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 7.31
r_work: 0.2885 rms_B_bonded: 6.86 restraints_weight: 2.0000
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5934  Z= 0.122
  Angle     :  0.531   6.847   8077  Z= 0.280
  Chirality :  0.044   0.138    874
  Planarity :  0.005   0.059   1047
  Dihedral  :  4.537  49.951    847
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.35 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.40 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.52 (0.31), residues: 740
  helix: -3.17 (0.63), residues: 50
  sheet: -0.05 (0.29), residues: 299
  loop : -0.05 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 452 
 TYR   0.013   0.001   TYR K 108 
 PHE   0.010   0.001   PHE L 141 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5923)
  covalent geometry    : angle       0.53031 ( 8054)
  SS BOND              : bond        0.00163 (   10)
  SS BOND              : angle       0.33307 (   20)
  hydrogen bonds       : bond        0.02962 (  198)
  hydrogen bonds       : angle       6.39476 (  576)
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       2.02694 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.196 
Fit side-chains
REVERT: L  144 ARG cc_start: 0.8645 (tpt-90) cc_final: 0.8418 (tpt-90)
REVERT: A  340 GLU cc_start: 0.8449 (tt0) cc_final: 0.8075 (tt0)
REVERT: A  382 VAL cc_start: 0.8929 (p) cc_final: 0.8691 (m)
REVERT: H   78 THR cc_start: 0.8921 (m) cc_final: 0.8443 (p)
REVERT: H  202 ASN cc_start: 0.7951 (m-40) cc_final: 0.7462 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 82
  average time/residue: 0.0892
  time to fit residues: 9.3790
Evaluate side-chains
  84 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   73 ASP
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.154172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.124454 restraints weight = 27468.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 7.37
r_work: 0.2851 rms_B_bonded: 6.89 restraints_weight: 2.0000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5934  Z= 0.140
  Angle     :  0.527   5.133   8077  Z= 0.278
  Chirality :  0.044   0.137    874
  Planarity :  0.005   0.059   1047
  Dihedral  :  4.479  48.191    847
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.76 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.62 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.45 (0.32), residues: 740
  helix: -3.14 (0.64), residues: 50
  sheet:  0.03 (0.29), residues: 299
  loop : -0.01 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 452 
 TYR   0.011   0.001   TYR K 108 
 PHE   0.011   0.001   PHE L 141 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5923)
  covalent geometry    : angle       0.52590 ( 8054)
  SS BOND              : bond        0.00180 (   10)
  SS BOND              : angle       0.33009 (   20)
  hydrogen bonds       : bond        0.02801 (  198)
  hydrogen bonds       : angle       5.97279 (  576)
  link_NAG-ASN         : bond        0.00125 (    1)
  link_NAG-ASN         : angle       1.86665 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.210 
Fit side-chains
REVERT: L  144 ARG cc_start: 0.8675 (tpt-90) cc_final: 0.8456 (tpt-90)
REVERT: A  340 GLU cc_start: 0.8397 (tt0) cc_final: 0.8019 (tt0)
REVERT: H   78 THR cc_start: 0.8950 (m) cc_final: 0.8485 (p)
REVERT: H   89 GLU cc_start: 0.8275 (pt0) cc_final: 0.8045 (pt0)
REVERT: H  202 ASN cc_start: 0.7923 (m-40) cc_final: 0.7436 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 84
  average time/residue: 0.0968
  time to fit residues: 10.1757
Evaluate side-chains
  84 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0970
   chunk 62 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0570
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.156508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.124483 restraints weight = 21007.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 6.48
r_work: 0.2938 rms_B_bonded: 6.12 restraints_weight: 2.0000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5934  Z= 0.124
  Angle     :  0.512   4.928   8077  Z= 0.271
  Chirality :  0.043   0.138    874
  Planarity :  0.004   0.058   1047
  Dihedral  :  4.419  47.450    847
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.21 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.94 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.44 (0.32), residues: 740
  helix: -3.11 (0.65), residues: 50
  sheet:  0.03 (0.29), residues: 301
  loop : -0.02 (0.34), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 452 
 TYR   0.009   0.001   TYR K 108 
 PHE   0.009   0.001   PHE L 141 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5923)
  covalent geometry    : angle       0.51190 ( 8054)
  SS BOND              : bond        0.00150 (   10)
  SS BOND              : angle       0.28879 (   20)
  hydrogen bonds       : bond        0.02608 (  198)
  hydrogen bonds       : angle       5.69329 (  576)
  link_NAG-ASN         : bond        0.00162 (    1)
  link_NAG-ASN         : angle       1.76088 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.248 
Fit side-chains
REVERT: L  144 ARG cc_start: 0.8591 (tpt-90) cc_final: 0.8368 (tpt-90)
REVERT: A  340 GLU cc_start: 0.8359 (tt0) cc_final: 0.7997 (tt0)
REVERT: H   78 THR cc_start: 0.8944 (m) cc_final: 0.8463 (p)
REVERT: H  202 ASN cc_start: 0.7859 (m-40) cc_final: 0.7439 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 85
  average time/residue: 0.0909
  time to fit residues: 9.9141
Evaluate side-chains
  83 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain K residue   35 SER
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 71 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0030
   chunk 20 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    0.3980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.3390

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.156095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.126299 restraints weight = 26865.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 7.21
r_work: 0.2900 rms_B_bonded: 6.96 restraints_weight: 2.0000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5934  Z= 0.102
  Angle     :  0.496   5.263   8077  Z= 0.261
  Chirality :  0.043   0.145    874
  Planarity :  0.004   0.057   1047
  Dihedral  :  4.283  46.443    847
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.21 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.89 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.25 (0.32), residues: 740
  helix: -3.10 (0.64), residues: 50
  sheet:  0.24 (0.30), residues: 289
  loop :  0.05 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  55 
 TYR   0.008   0.001   TYR K 108 
 PHE   0.010   0.001   PHE L 141 
 TRP   0.007   0.001   TRP H 106 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 5923)
  covalent geometry    : angle       0.49591 ( 8054)
  SS BOND              : bond        0.00122 (   10)
  SS BOND              : angle       0.25624 (   20)
  hydrogen bonds       : bond        0.02437 (  198)
  hydrogen bonds       : angle       5.40249 (  576)
  link_NAG-ASN         : bond        0.00191 (    1)
  link_NAG-ASN         : angle       1.59902 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.202 
Fit side-chains
REVERT: L  144 ARG cc_start: 0.8613 (tpt-90) cc_final: 0.8372 (tpt-90)
REVERT: A  340 GLU cc_start: 0.8340 (tt0) cc_final: 0.7983 (tt0)
REVERT: H   78 THR cc_start: 0.8852 (m) cc_final: 0.8463 (p)
REVERT: H  202 ASN cc_start: 0.7914 (m-40) cc_final: 0.7582 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 83
  average time/residue: 0.0889
  time to fit residues: 9.4594
Evaluate side-chains
  79 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0980
   chunk 49 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.152930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.122713 restraints weight = 23507.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 6.41
r_work: 0.2867 rms_B_bonded: 6.33 restraints_weight: 2.0000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5934  Z= 0.164
  Angle     :  0.538   5.799   8077  Z= 0.284
  Chirality :  0.044   0.146    874
  Planarity :  0.005   0.059   1047
  Dihedral  :  4.449  47.043    847
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.48 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.52 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.41 (0.32), residues: 740
  helix: -3.08 (0.66), residues: 50
  sheet:  0.06 (0.29), residues: 303
  loop : -0.00 (0.34), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 452 
 TYR   0.013   0.001   TYR A 473 
 PHE   0.011   0.001   PHE A 400 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 5923)
  covalent geometry    : angle       0.53780 ( 8054)
  SS BOND              : bond        0.00209 (   10)
  SS BOND              : angle       0.39973 (   20)
  hydrogen bonds       : bond        0.02722 (  198)
  hydrogen bonds       : angle       5.53552 (  576)
  link_NAG-ASN         : bond        0.00161 (    1)
  link_NAG-ASN         : angle       1.67376 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.224 
Fit side-chains
REVERT: L  144 ARG cc_start: 0.8629 (tpt-90) cc_final: 0.8377 (tpt-90)
REVERT: A  340 GLU cc_start: 0.8364 (tt0) cc_final: 0.7986 (tt0)
REVERT: H   78 THR cc_start: 0.8977 (m) cc_final: 0.8524 (p)
REVERT: H  202 ASN cc_start: 0.8002 (m-40) cc_final: 0.7561 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 80
  average time/residue: 0.0896
  time to fit residues: 9.1692
Evaluate side-chains
  81 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain K residue   35 SER
Chi-restraints excluded: chain K residue   73 ASP
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.149799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.121675 restraints weight = 27778.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 6.00
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5934  Z= 0.236
  Angle     :  0.606   6.773   8077  Z= 0.320
  Chirality :  0.046   0.152    874
  Planarity :  0.005   0.060   1047
  Dihedral  :  4.856  46.291    847
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.43 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.68 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.58 (0.32), residues: 740
  helix: -2.83 (0.76), residues: 42
  sheet: -0.21 (0.28), residues: 308
  loop : -0.09 (0.35), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 452 
 TYR   0.017   0.002   TYR A 473 
 PHE   0.014   0.002   PHE A 400 
 TRP   0.012   0.002   TRP A 436 
 HIS   0.005   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 5923)
  covalent geometry    : angle       0.60539 ( 8054)
  SS BOND              : bond        0.00304 (   10)
  SS BOND              : angle       0.55613 (   20)
  hydrogen bonds       : bond        0.03084 (  198)
  hydrogen bonds       : angle       5.88955 (  576)
  link_NAG-ASN         : bond        0.00152 (    1)
  link_NAG-ASN         : angle       2.02256 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8105 (tt0) cc_final: 0.7673 (tt0)
REVERT: A  478 LYS cc_start: 0.7658 (mmtm) cc_final: 0.7339 (mmtm)
REVERT: H   78 THR cc_start: 0.8890 (m) cc_final: 0.8664 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 87
  average time/residue: 0.0956
  time to fit residues: 10.6441
Evaluate side-chains
  83 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 42 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0470
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.157588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.125112 restraints weight = 20161.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 6.86
r_work: 0.2919 rms_B_bonded: 6.10 restraints_weight: 2.0000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5934  Z= 0.141
  Angle     :  0.542   5.534   8077  Z= 0.285
  Chirality :  0.044   0.145    874
  Planarity :  0.005   0.058   1047
  Dihedral  :  4.622  46.596    847
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.35 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.47 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.57 (0.32), residues: 740
  helix: -2.94 (0.74), residues: 42
  sheet: -0.10 (0.29), residues: 302
  loop : -0.18 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  18 
 TYR   0.011   0.001   TYR A 473 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.008   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5923)
  covalent geometry    : angle       0.53947 ( 8054)
  SS BOND              : bond        0.00244 (   10)
  SS BOND              : angle       0.93108 (   20)
  hydrogen bonds       : bond        0.02677 (  198)
  hydrogen bonds       : angle       5.64063 (  576)
  link_NAG-ASN         : bond        0.00211 (    1)
  link_NAG-ASN         : angle       1.88269 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8403 (tt0) cc_final: 0.7981 (tt0)
REVERT: H   78 THR cc_start: 0.8997 (m) cc_final: 0.8583 (p)
REVERT: H  202 ASN cc_start: 0.7931 (t0) cc_final: 0.7695 (m110)
  outliers start: 9
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0983
  time to fit residues: 9.6906
Evaluate side-chains
  77 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain K residue   73 ASP
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 29 optimal weight:    0.1980
   chunk 9 optimal weight:    0.5980
   chunk 41 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:    0.2980
   chunk 0 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.157068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.129748 restraints weight = 29102.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 6.99
r_work: 0.2918 rms_B_bonded: 6.88 restraints_weight: 2.0000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2850
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5934  Z= 0.113
  Angle     :  0.517   5.074   8077  Z= 0.272
  Chirality :  0.043   0.141    874
  Planarity :  0.004   0.058   1047
  Dihedral  :  4.421  45.155    847
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.35 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.79 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.49 (0.32), residues: 740
  helix: -3.22 (0.64), residues: 50
  sheet:  0.04 (0.29), residues: 298
  loop : -0.08 (0.34), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  18 
 TYR   0.009   0.001   TYR A 351 
 PHE   0.007   0.001   PHE A 400 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5923)
  covalent geometry    : angle       0.51581 ( 8054)
  SS BOND              : bond        0.00143 (   10)
  SS BOND              : angle       0.48206 (   20)
  hydrogen bonds       : bond        0.02478 (  198)
  hydrogen bonds       : angle       5.39164 (  576)
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       1.69322 (    3)

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

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

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1480 Ramachandran restraints generated.
    740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8374 (tt0) cc_final: 0.7979 (tt0)
REVERT: H   78 THR cc_start: 0.8934 (m) cc_final: 0.8448 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 80
  average time/residue: 0.0966
  time to fit residues: 9.9202
Evaluate side-chains
  79 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain K residue   73 ASP
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   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 = 0.3759 r_free = 0.3759 target = 0.153369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121448 restraints weight = 20614.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 7.08
r_work: 0.2893 rms_B_bonded: 6.14 restraints_weight: 2.0000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5934  Z= 0.151
  Angle     :  0.536   5.924   8077  Z= 0.281
  Chirality :  0.044   0.144    874
  Planarity :  0.005   0.059   1047
  Dihedral  :  4.482  45.550    847
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.21 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.79 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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 are not related in a simple way.
  whole: -0.54 (0.32), residues: 740
  helix: -3.18 (0.65), residues: 50
  sheet: -0.03 (0.29), residues: 294
  loop : -0.09 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  18 
 TYR   0.015   0.001   TYR A 351 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5923)
  covalent geometry    : angle       0.53555 ( 8054)
  SS BOND              : bond        0.00202 (   10)
  SS BOND              : angle       0.46977 (   20)
  hydrogen bonds       : bond        0.02616 (  198)
  hydrogen bonds       : angle       5.46162 (  576)
  link_NAG-ASN         : bond        0.00158 (    1)
  link_NAG-ASN         : angle       1.72717 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1624.77 seconds
wall clock time: 28 minutes 44.50 seconds (1724.50 seconds total)