Starting phenix.real_space_refine
on Sat May  2 13:32:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11ol_75887/05_2026/11ol_75887.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11ol_75887/05_2026/11ol_75887.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/11ol_75887/05_2026/11ol_75887.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11ol_75887/05_2026/11ol_75887.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/11ol_75887/05_2026/11ol_75887.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11ol_75887/05_2026/11ol_75887.cif"
  }
  resolution = 3.2
  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=   0.008
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    3655      2.51       5
     N     994      2.21       5
     O    1128      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: 5801
  Number of models: 1
  Model: ""
    Number of chains: 5
    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: "H"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1627
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "L"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1649
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203}
    Chain: "K"
      Number of atoms: 928
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
      Conformer: "B"
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          bond proxies already assigned to first conformer: 940
    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=0.19
      ... (14 atoms not shown)
      pdb=" ND2BASN A 450 " occ=0.81
  Time building chain proxies: 2.13, per 1000 atoms: 0.37
  Number of scatterers: 5801
  At special positions: 0
  Unit cell: (75.816, 83.304, 123.552, 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    1128      8.00
     N     994      7.00
     C    3655      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    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 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
    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 K  22 " - pdb=" SG  CYS K  96 " 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: 0.48
  Conformation dependent library (CDL) restraints added in 491.5 milliseconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 18 sheets defined
      10.9% alpha, 38.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.534A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
    Processing helix  chain 'A' and resid 384 through 389
      removed outlier: 3.624A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.923A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    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 189 through 195
      removed outlier: 4.104A  pdb=" N   GLY H 193 " --> pdb=" O   SER H 189 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   THR H 194 " --> pdb=" O   SER H 190 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 204 through 207
    Processing helix  chain 'L' and resid 123 through 128
    Processing helix  chain 'L' and resid 185 through 190
    Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 363
      removed outlier: 3.620A  pdb=" N   CYS A 525 " --> pdb=" O   CYS A 361 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 380
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.588A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.548A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 123 through 127
      removed outlier: 3.523A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 123 through 127
      removed outlier: 3.523A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 154 through 157
      removed outlier: 4.428A  pdb=" N   TYR H 197 " --> pdb=" O   VAL H 214 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL H 210 " --> pdb=" O   VAL H 201 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.550A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.640A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 22
      removed outlier: 3.636A  pdb=" N   ASP L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120
      removed outlier: 3.797A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 152
    Processing sheet with id=AB6, first strand: chain 'K' and resid 21 through 23
    Processing sheet with id=AB7, first strand: chain 'K' and resid 46 through 47
      removed outlier: 3.533A  pdb=" N   GLU K  46 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA K  97 " --> pdb=" O   SER K  35 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   TYR K 110 " --> pdb=" O   ILE K  98 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'K' and resid 46 through 47
      removed outlier: 3.533A  pdb=" N   GLU K  46 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA K  97 " --> pdb=" O   SER K  35 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL K 117 " --> pdb=" O   ALA K  92 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'K' and resid 49 through 51

    216 hydrogen bonds defined for protein.
    525 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: 0.97

  Time building geometry restraints manager: 0.67 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: 1880
        1.34 -     1.46: 1325
        1.46 -     1.58: 2713
        1.58 -     1.69: 2
        1.69 -     1.81: 29
  Bond restraints: 5949
  Sorted by residual:
  bond pdb=" C   SER K   7 "
       pdb=" O   SER K   7 "
    ideal  model  delta    sigma   weight residual
    1.235  1.350 -0.115 1.26e-02 6.30e+03 8.30e+01
  bond pdb=" C   SER K   7 "
       pdb=" CA ASER K   7 "
    ideal  model  delta    sigma   weight residual
    1.523  1.599 -0.076 1.34e-02 5.57e+03 3.21e+01
  bond pdb=" C   SER K   7 "
       pdb=" CA BSER K   7 "
    ideal  model  delta    sigma   weight residual
    1.523  1.599 -0.076 1.34e-02 5.57e+03 3.21e+01
  bond pdb=" N   SER K   7 "
       pdb=" CA ASER K   7 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.61e+00
  bond pdb=" N   SER K   7 "
       pdb=" CA BSER K   7 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.61e+00
  ... (remaining 5944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 8025
        2.51 -     5.01: 57
        5.01 -     7.52: 5
        7.52 -    10.03: 4
       10.03 -    12.54: 2
  Bond angle restraints: 8093
  Sorted by residual:
  angle pdb=" O   SER K   7 "
        pdb=" C   SER K   7 "
        pdb=" CA ASER K   7 "
      ideal   model   delta    sigma   weight residual
     120.51  133.05  -12.54 1.43e+00 4.89e-01 7.69e+01
  angle pdb=" O   SER K   7 "
        pdb=" C   SER K   7 "
        pdb=" CA BSER K   7 "
      ideal   model   delta    sigma   weight residual
     120.51  133.05  -12.54 1.43e+00 4.89e-01 7.69e+01
  angle pdb=" O   SER K   7 "
        pdb=" C   SER K   7 "
        pdb=" N   GLY K   8 "
      ideal   model   delta    sigma   weight residual
     122.59  114.80    7.79 1.33e+00 5.65e-01 3.43e+01
  angle pdb=" C   SER K   7 "
        pdb=" N   GLY K   8 "
        pdb=" CA  GLY K   8 "
      ideal   model   delta    sigma   weight residual
     120.43  115.92    4.51 1.06e+00 8.90e-01 1.81e+01
  angle pdb=" N   SER K   7 "
        pdb=" CA ASER K   7 "
        pdb=" C   SER K   7 "
      ideal   model   delta    sigma   weight residual
     110.80  119.83   -9.03 2.13e+00 2.20e-01 1.80e+01
  ... (remaining 8088 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 3208
       16.24 -    32.47: 269
       32.47 -    48.70: 44
       48.70 -    64.94: 10
       64.94 -    81.17: 9
  Dihedral angle restraints: 3540
    sinusoidal: 1367
      harmonic: 2173
  Sorted by residual:
  dihedral pdb=" CA  PHE K 103 "
           pdb=" C   PHE K 103 "
           pdb=" N   TYR K 104 "
           pdb=" CA  TYR K 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.29   17.71     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   64.12   28.88     1      1.00e+01 1.00e-02 1.19e+01
  dihedral pdb=" CB  CYS L 136 "
           pdb=" SG  CYS L 136 "
           pdb=" SG  CYS L 196 "
           pdb=" CB  CYS L 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   66.55   26.45     1      1.00e+01 1.00e-02 1.00e+01
  ... (remaining 3537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 625
       0.040 -    0.080: 169
       0.080 -    0.120: 75
       0.120 -    0.160: 7
       0.160 -    0.200: 1
  Chirality restraints: 877
  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 1.00e+00
  chirality pdb=" CA  VAL L 134 "
            pdb=" N   VAL L 134 "
            pdb=" C   VAL L 134 "
            pdb=" CB  VAL L 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 874 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 151 "    0.029 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO H 152 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO H 152 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 152 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO A 463 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 372 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A 373 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 373 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 373 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 3106
        3.01 -     3.48: 5400
        3.48 -     3.96: 9134
        3.96 -     4.43: 10723
        4.43 -     4.90: 17924
  Nonbonded interactions: 46287
  Sorted by model distance:
  nonbonded pdb=" O   SER K   7 "
            pdb=" CA  GLY K   8 "
     model   vdw
     2.539 2.752
  nonbonded pdb=" C   SER K   7 "
            pdb=" OG ASER K   7 "
     model   vdw
     2.560 2.616
  nonbonded pdb=" C   SER K   7 "
            pdb=" OG BSER K   7 "
     model   vdw
     2.561 2.616
  nonbonded pdb=" OG BSER K   7 "
            pdb=" O   ARG K  19 "
     model   vdw
     2.577 3.040
  nonbonded pdb=" OG ASER K   7 "
            pdb=" O   ARG K  19 "
     model   vdw
     2.578 3.040
  ... (remaining 46282 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=0.04 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:             6.960
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.310
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
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   0.115   5959  Z= 0.217
  Angle     :  0.624  12.537   8114  Z= 0.346
  Chirality :  0.044   0.200    877
  Planarity :  0.005   0.045   1055
  Dihedral  : 12.843  81.174   2135
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.18 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  0.00 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.31 (0.32), residues: 747
  helix: -1.81 (0.96), residues: 33
  sheet: -0.16 (0.33), residues: 268
  loop :  0.00 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 346 
 TYR   0.022   0.002   TYR A 453 
 PHE   0.025   0.001   PHE A 347 
 TRP   0.013   0.001   TRP L 150 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5949)
  covalent geometry    : angle       0.62361 ( 8093)
  SS BOND              : bond        0.00139 (    9)
  SS BOND              : angle       0.75046 (   18)
  hydrogen bonds       : bond        0.24472 (  190)
  hydrogen bonds       : angle      10.57337 (  525)
  link_NAG-ASN         : bond        0.00114 (    1)
  link_NAG-ASN         : angle       1.33193 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.7340 (m-40) cc_final: 0.6865 (t0)
REVERT: H   21 SER cc_start: 0.8339 (t) cc_final: 0.8042 (p)
REVERT: L   24 ARG cc_start: 0.7467 (ptp-170) cc_final: 0.7266 (mtm110)
REVERT: L  149 GLN cc_start: 0.7068 (mt0) cc_final: 0.6707 (mt0)
  outliers start: 2
  outliers final: 1
  residues processed: 116
  average time/residue: 0.1051
  time to fit residues: 14.9777
Evaluate side-chains
  96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    6 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
H  74 ASN
H 167 HIS
L 139 ASN
L 201 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.167275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.134171 restraints weight = 23337.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 7.58
r_work: 0.3088 rms_B_bonded: 6.31 restraints_weight: 2.0000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5959  Z= 0.223
  Angle     :  0.624   7.335   8114  Z= 0.323
  Chirality :  0.046   0.139    877
  Planarity :  0.005   0.045   1055
  Dihedral  :  5.152  48.164    857
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  6.97 %
    Favored  : 92.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.47 (0.32), residues: 747
  helix: -2.14 (0.90), residues: 35
  sheet: -0.22 (0.32), residues: 279
  loop : -0.09 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 346 
 TYR   0.020   0.002   TYR A 495 
 PHE   0.039   0.002   PHE A 347 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.012   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 5949)
  covalent geometry    : angle       0.62225 ( 8093)
  SS BOND              : bond        0.00253 (    9)
  SS BOND              : angle       0.97982 (   18)
  hydrogen bonds       : bond        0.03967 (  190)
  hydrogen bonds       : angle       7.18208 (  525)
  link_NAG-ASN         : bond        0.00179 (    1)
  link_NAG-ASN         : angle       1.21572 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.7379 (m-40) cc_final: 0.6900 (t0)
REVERT: L   24 ARG cc_start: 0.8085 (ptp-170) cc_final: 0.7579 (mtm110)
  outliers start: 4
  outliers final: 3
  residues processed: 93
  average time/residue: 0.1046
  time to fit residues: 12.1738
Evaluate side-chains
  88 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  198 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0970
   chunk 46 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
L 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.164455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.132387 restraints weight = 28683.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 9.22
r_work: 0.3050 rms_B_bonded: 6.84 restraints_weight: 2.0000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5959  Z= 0.190
  Angle     :  0.588   7.621   8114  Z= 0.303
  Chirality :  0.044   0.143    877
  Planarity :  0.005   0.043   1055
  Dihedral  :  4.551  19.339    854
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.14 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.53 (0.32), residues: 747
  helix: -2.00 (0.93), residues: 34
  sheet: -0.20 (0.32), residues: 278
  loop : -0.21 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 452 
 TYR   0.017   0.002   TYR A 495 
 PHE   0.029   0.002   PHE A 347 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 5949)
  covalent geometry    : angle       0.58709 ( 8093)
  SS BOND              : bond        0.00212 (    9)
  SS BOND              : angle       0.76415 (   18)
  hydrogen bonds       : bond        0.03639 (  190)
  hydrogen bonds       : angle       6.60655 (  525)
  link_NAG-ASN         : bond        0.00078 (    1)
  link_NAG-ASN         : angle       1.31386 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  370 ASN cc_start: 0.7917 (m-40) cc_final: 0.7684 (m-40)
REVERT: A  438 SER cc_start: 0.9205 (p) cc_final: 0.8788 (p)
REVERT: A  487 ASN cc_start: 0.7355 (m-40) cc_final: 0.6708 (t0)
REVERT: H  213 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7286 (ttt180)
REVERT: L   24 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7692 (mtm110)
  outliers start: 4
  outliers final: 3
  residues processed: 92
  average time/residue: 0.1234
  time to fit residues: 13.6653
Evaluate side-chains
  90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  198 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0670
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3913 r_free = 0.3913 target = 0.166935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135460 restraints weight = 29290.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 8.33
r_work: 0.3081 rms_B_bonded: 6.84 restraints_weight: 2.0000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5959  Z= 0.123
  Angle     :  0.534   7.653   8114  Z= 0.276
  Chirality :  0.043   0.130    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.244  19.202    854
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.09 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.40 (0.32), residues: 747
  helix: -2.11 (0.91), residues: 35
  sheet: -0.12 (0.32), residues: 280
  loop : -0.08 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K  38 
 TYR   0.013   0.001   TYR K 104 
 PHE   0.016   0.001   PHE A 347 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5949)
  covalent geometry    : angle       0.53356 ( 8093)
  SS BOND              : bond        0.00283 (    9)
  SS BOND              : angle       0.68176 (   18)
  hydrogen bonds       : bond        0.03084 (  190)
  hydrogen bonds       : angle       6.12978 (  525)
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.35862 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.7302 (m-40) cc_final: 0.6603 (t0)
REVERT: L   24 ARG cc_start: 0.8183 (ptp-170) cc_final: 0.7715 (mtm110)
  outliers start: 4
  outliers final: 4
  residues processed: 87
  average time/residue: 0.0927
  time to fit residues: 10.2175
Evaluate side-chains
  84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3923 r_free = 0.3923 target = 0.167398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.133652 restraints weight = 20102.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 6.41
r_work: 0.3128 rms_B_bonded: 5.79 restraints_weight: 2.0000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5959  Z= 0.153
  Angle     :  0.550   7.627   8114  Z= 0.283
  Chirality :  0.043   0.133    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.284  19.648    854
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.83 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.40 (0.32), residues: 747
  helix: -1.87 (0.96), residues: 34
  sheet: -0.20 (0.31), residues: 297
  loop : -0.04 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  38 
 TYR   0.013   0.002   TYR H  51 
 PHE   0.020   0.001   PHE A 347 
 TRP   0.008   0.001   TRP H 157 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5949)
  covalent geometry    : angle       0.54880 ( 8093)
  SS BOND              : bond        0.00214 (    9)
  SS BOND              : angle       0.69422 (   18)
  hydrogen bonds       : bond        0.03091 (  190)
  hydrogen bonds       : angle       5.91832 (  525)
  link_NAG-ASN         : bond        0.00089 (    1)
  link_NAG-ASN         : angle       1.39758 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.7278 (m-40) cc_final: 0.6664 (t0)
REVERT: H    2 VAL cc_start: 0.7795 (t) cc_final: 0.7494 (t)
REVERT: L   24 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.7862 (mtm110)
  outliers start: 11
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1090
  time to fit residues: 11.7948
Evaluate side-chains
  84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  198 ILE
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   chunk 34 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 52 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3919 r_free = 0.3919 target = 0.167056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.133808 restraints weight = 24138.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 7.18
r_work: 0.3108 rms_B_bonded: 6.14 restraints_weight: 2.0000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5959  Z= 0.140
  Angle     :  0.542   7.515   8114  Z= 0.277
  Chirality :  0.043   0.132    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.236  19.279    854
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.46 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.35 (0.32), residues: 747
  helix: -1.75 (0.98), residues: 34
  sheet: -0.17 (0.31), residues: 297
  loop :  0.00 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K  38 
 TYR   0.014   0.002   TYR K 104 
 PHE   0.017   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5949)
  covalent geometry    : angle       0.54143 ( 8093)
  SS BOND              : bond        0.00184 (    9)
  SS BOND              : angle       0.63773 (   18)
  hydrogen bonds       : bond        0.02946 (  190)
  hydrogen bonds       : angle       5.74429 (  525)
  link_NAG-ASN         : bond        0.00087 (    1)
  link_NAG-ASN         : angle       1.43463 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.7253 (m-40) cc_final: 0.6582 (t0)
REVERT: H    2 VAL cc_start: 0.7607 (t) cc_final: 0.7366 (t)
REVERT: L   24 ARG cc_start: 0.8190 (ptp-170) cc_final: 0.7749 (mtm110)
  outliers start: 7
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1051
  time to fit residues: 11.0071
Evaluate side-chains
  85 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  198 ILE
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0980
   chunk 68 optimal weight:    0.7980
   chunk 32 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0570
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.168931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.135496 restraints weight = 24370.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 7.27
r_work: 0.3138 rms_B_bonded: 6.26 restraints_weight: 2.0000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5959  Z= 0.105
  Angle     :  0.516   6.961   8114  Z= 0.264
  Chirality :  0.042   0.128    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.024  18.831    854
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.46 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.24 (0.32), residues: 747
  helix: -1.75 (0.97), residues: 34
  sheet: -0.11 (0.31), residues: 299
  loop :  0.09 (0.33), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  38 
 TYR   0.013   0.001   TYR K 104 
 PHE   0.013   0.001   PHE A 375 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5949)
  covalent geometry    : angle       0.51552 ( 8093)
  SS BOND              : bond        0.00203 (    9)
  SS BOND              : angle       0.59200 (   18)
  hydrogen bonds       : bond        0.02742 (  190)
  hydrogen bonds       : angle       5.53525 (  525)
  link_NAG-ASN         : bond        0.00063 (    1)
  link_NAG-ASN         : angle       1.45134 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.7262 (m-40) cc_final: 0.6603 (t0)
REVERT: H    2 VAL cc_start: 0.7554 (t) cc_final: 0.7316 (t)
REVERT: L   24 ARG cc_start: 0.8264 (ptp-170) cc_final: 0.7770 (mtm110)
  outliers start: 8
  outliers final: 5
  residues processed: 86
  average time/residue: 0.1060
  time to fit residues: 11.4080
Evaluate side-chains
  83 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3915 r_free = 0.3915 target = 0.166668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.132552 restraints weight = 24288.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 7.36
r_work: 0.3103 rms_B_bonded: 6.00 restraints_weight: 2.0000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5959  Z= 0.173
  Angle     :  0.563   7.429   8114  Z= 0.288
  Chirality :  0.044   0.136    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.275  19.642    854
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.25 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.35 (0.32), residues: 747
  helix: -1.72 (0.99), residues: 34
  sheet: -0.27 (0.30), residues: 305
  loop :  0.08 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K  38 
 TYR   0.011   0.002   TYR A 380 
 PHE   0.019   0.001   PHE A 347 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 5949)
  covalent geometry    : angle       0.56131 ( 8093)
  SS BOND              : bond        0.00166 (    9)
  SS BOND              : angle       0.82292 (   18)
  hydrogen bonds       : bond        0.03021 (  190)
  hydrogen bonds       : angle       5.71746 (  525)
  link_NAG-ASN         : bond        0.00095 (    1)
  link_NAG-ASN         : angle       1.45510 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 ASN cc_start: 0.7303 (m-40) cc_final: 0.6603 (t0)
REVERT: H    2 VAL cc_start: 0.7711 (t) cc_final: 0.7443 (t)
REVERT: L   24 ARG cc_start: 0.8220 (ptp-170) cc_final: 0.7784 (mtm110)
  outliers start: 5
  outliers final: 5
  residues processed: 82
  average time/residue: 0.1013
  time to fit residues: 10.3734
Evaluate side-chains
  84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  198 ILE
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0020
   chunk 38 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0000
   chunk 37 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3921 r_free = 0.3921 target = 0.167293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.135060 restraints weight = 21482.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 7.12
r_work: 0.3129 rms_B_bonded: 6.13 restraints_weight: 2.0000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5959  Z= 0.122
  Angle     :  0.529   6.991   8114  Z= 0.270
  Chirality :  0.042   0.130    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.115  19.189    854
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.57 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.24 (0.32), residues: 747
  helix: -1.81 (0.97), residues: 34
  sheet: -0.18 (0.30), residues: 303
  loop :  0.16 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  38 
 TYR   0.013   0.001   TYR K 104 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5949)
  covalent geometry    : angle       0.52739 ( 8093)
  SS BOND              : bond        0.00168 (    9)
  SS BOND              : angle       0.75560 (   18)
  hydrogen bonds       : bond        0.02815 (  190)
  hydrogen bonds       : angle       5.58616 (  525)
  link_NAG-ASN         : bond        0.00074 (    1)
  link_NAG-ASN         : angle       1.42528 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  409 GLN cc_start: 0.8120 (mt0) cc_final: 0.7663 (mt0)
REVERT: A  487 ASN cc_start: 0.7267 (m-40) cc_final: 0.6601 (t0)
REVERT: H    2 VAL cc_start: 0.7686 (t) cc_final: 0.7411 (t)
REVERT: L   24 ARG cc_start: 0.8267 (ptp-170) cc_final: 0.7761 (mtm110)
  outliers start: 5
  outliers final: 5
  residues processed: 80
  average time/residue: 0.1172
  time to fit residues: 11.4764
Evaluate side-chains
  83 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  198 ILE
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0670
   chunk 21 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0020
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.5326

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3923 r_free = 0.3923 target = 0.167522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.135480 restraints weight = 25230.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 7.58
r_work: 0.3129 rms_B_bonded: 6.49 restraints_weight: 2.0000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5959  Z= 0.123
  Angle     :  0.530   6.975   8114  Z= 0.270
  Chirality :  0.042   0.130    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.072  18.946    854
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.41 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.24 (0.32), residues: 747
  helix: -1.76 (0.98), residues: 34
  sheet: -0.19 (0.30), residues: 305
  loop :  0.17 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  38 
 TYR   0.014   0.001   TYR K 104 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5949)
  covalent geometry    : angle       0.52916 ( 8093)
  SS BOND              : bond        0.00159 (    9)
  SS BOND              : angle       0.73324 (   18)
  hydrogen bonds       : bond        0.02789 (  190)
  hydrogen bonds       : angle       5.56203 (  525)
  link_NAG-ASN         : bond        0.00073 (    1)
  link_NAG-ASN         : angle       1.45246 (    3)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  409 GLN cc_start: 0.8112 (mt0) cc_final: 0.7668 (mt0)
REVERT: A  487 ASN cc_start: 0.7270 (m-40) cc_final: 0.6583 (t0)
REVERT: H    2 VAL cc_start: 0.7674 (t) cc_final: 0.7408 (t)
REVERT: L   24 ARG cc_start: 0.8268 (ptp-170) cc_final: 0.7752 (mtm110)
  outliers start: 6
  outliers final: 5
  residues processed: 79
  average time/residue: 0.1095
  time to fit residues: 10.6675
Evaluate side-chains
  81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  198 ILE
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0670
   chunk 71 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0470
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.3925 r_free = 0.3925 target = 0.167650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135233 restraints weight = 26936.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 8.26
r_work: 0.3094 rms_B_bonded: 6.84 restraints_weight: 2.0000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5959  Z= 0.152
  Angle     :  0.549   7.313   8114  Z= 0.280
  Chirality :  0.043   0.133    877
  Planarity :  0.004   0.043   1055
  Dihedral  :  4.200  19.113    854
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.57 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.29 (0.32), residues: 747
  helix: -1.76 (0.97), residues: 34
  sheet: -0.24 (0.30), residues: 305
  loop :  0.16 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K  38 
 TYR   0.015   0.002   TYR K 104 
 PHE   0.018   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5949)
  covalent geometry    : angle       0.54774 ( 8093)
  SS BOND              : bond        0.00168 (    9)
  SS BOND              : angle       0.77525 (   18)
  hydrogen bonds       : bond        0.02901 (  190)
  hydrogen bonds       : angle       5.63862 (  525)
  link_NAG-ASN         : bond        0.00097 (    1)
  link_NAG-ASN         : angle       1.42223 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1834.13 seconds
wall clock time: 32 minutes 6.26 seconds (1926.26 seconds total)