Starting phenix.real_space_refine
on Fri Aug 22 15:55:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bd8_44446/08_2025/9bd8_44446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bd8_44446/08_2025/9bd8_44446.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bd8_44446/08_2025/9bd8_44446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bd8_44446/08_2025/9bd8_44446.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bd8_44446/08_2025/9bd8_44446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bd8_44446/08_2025/9bd8_44446.cif"
  }
  resolution = 4.8
  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=   0.003
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      20      5.16       5
     C    3406      2.51       5
     N     880      2.21       5
     O    1063      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5369
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3423
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 24, 'TRANS': 437}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 175
          Unresolved non-hydrogen angles: 193
          Unresolved non-hydrogen dihedrals: 164
          Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 65
    Chain: "B"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1932
          Classifications: {'peptide': 264}
          Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 9, 'TRANS': 254}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 226
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 12, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 1, 'GLU:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 106
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.36, per 1000 atoms: 0.25
  Number of scatterers: 5369
  At special positions: 0
  Unit cell: (61.42, 94.62, 129.48, 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      20     16.00
     O    1063      8.00
     N     880      7.00
     C    3406      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  39 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 186 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 245 " - pdb=" SG  CYS A 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 385 " - pdb=" SG  CYS A 390 " 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 A4601 " - " ASN A 185 "
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 214.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1360

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 9 sheets defined
      14.2% alpha, 29.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 129
      removed outlier: 4.327A  pdb=" N   TYR A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 139
    Processing helix  chain 'A' and resid 150 through 165
    Processing helix  chain 'A' and resid 232 through 238
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 3.832A  pdb=" N   ASN A 274 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 320
      No H-bonds generated for 'chain 'A' and resid 318 through 320'
    Processing helix  chain 'A' and resid 321 through 330
      removed outlier: 3.872A  pdb=" N   VAL A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 334
    Processing helix  chain 'A' and resid 343 through 357
    Processing helix  chain 'A' and resid 359 through 365
    Processing helix  chain 'A' and resid 375 through 384
      removed outlier: 3.863A  pdb=" N   GLN A 380 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ALA A 381 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 393
      removed outlier: 4.282A  pdb=" N   THR A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   HIS A 393 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 506
      No H-bonds generated for 'chain 'B' and resid 504 through 506'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 51 through 58
    current: chain 'A' and resid 72 through 83
      removed outlier: 6.836A  pdb=" N   ALA A  73 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLU A 101 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ARG A  75 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LEU A  99 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASN A  77 " --> pdb=" O   CYS A  97 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   CYS A  97 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU A 112 " --> pdb=" O   TYR A 103 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 111 through 115
    current: chain 'A' and resid 142 through 144
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 142 through 144
    current: chain 'A' and resid 186 through 195
      removed outlier: 5.912A  pdb=" N   SER A 187 " --> pdb=" O   ASP A 208 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   ASP A 208 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLU A 206 " --> pdb=" O   HIS A 189 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   GLU A 202 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ARG A 195 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ALA A 200 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 829 through 839
      removed outlier: 4.938A  pdb=" N   ILE A 830 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE A 854 " --> pdb=" O   ILE A 830 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLN A 845 " --> pdb=" O   ILE A 890 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LEU A 942 " --> pdb=" O   ILE A 953 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 961 through 962
    Processing sheet with id=AA4, first strand: chain 'B' and resid 401 through 405
      removed outlier: 6.085A  pdb=" N   LYS B 411 " --> pdb=" O   SER B 421 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   SER B 421 " --> pdb=" O   LYS B 411 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 443
    Processing sheet with id=AA6, first strand: chain 'B' and resid 476 through 482
      removed outlier: 3.942A  pdb=" N   GLY B 478 " --> pdb=" O   THR B 491 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR B 491 " --> pdb=" O   GLY B 478 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 518 through 524
      removed outlier: 5.921A  pdb=" N   THR B 534 " --> pdb=" O   ARG B 520 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ILE B 522 " --> pdb=" O   TYR B 532 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   TYR B 532 " --> pdb=" O   ILE B 522 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 563 through 568
      removed outlier: 6.591A  pdb=" N   VAL B 578 " --> pdb=" O   ASN B 564 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ILE B 566 " --> pdb=" O   TYR B 576 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   TYR B 576 " --> pdb=" O   ILE B 566 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 612 through 614

    181 hydrogen bonds defined for protein.
    474 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: 0.87

  Time building geometry restraints manager: 0.60 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: 1760
        1.34 -     1.46: 1227
        1.46 -     1.58: 2460
        1.58 -     1.70: 0
        1.70 -     1.82: 28
  Bond restraints: 5475
  Sorted by residual:
  bond pdb=" CA  SER B 648 "
       pdb=" C   SER B 648 "
    ideal  model  delta    sigma   weight residual
    1.531  1.523  0.008 7.40e-03 1.83e+04 1.30e+00
  bond pdb=" CA  SER B 648 "
       pdb=" CB  SER B 648 "
    ideal  model  delta    sigma   weight residual
    1.522  1.529 -0.007 7.00e-03 2.04e+04 1.01e+00
  bond pdb=" N   ALA B 437 "
       pdb=" CA  ALA B 437 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.012 1.29e-02 6.01e+03 8.85e-01
  bond pdb=" N   ASN B 425 "
       pdb=" CA  ASN B 425 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.010 1.29e-02 6.01e+03 6.35e-01
  bond pdb=" CB  PRO B 519 "
       pdb=" CG  PRO B 519 "
    ideal  model  delta    sigma   weight residual
    1.492  1.530 -0.038 5.00e-02 4.00e+02 5.88e-01
  ... (remaining 5470 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 7141
        1.32 -     2.63: 282
        2.63 -     3.95: 47
        3.95 -     5.26: 10
        5.26 -     6.58: 6
  Bond angle restraints: 7486
  Sorted by residual:
  angle pdb=" C   ALA B 437 "
        pdb=" CA  ALA B 437 "
        pdb=" CB  ALA B 437 "
      ideal   model   delta    sigma   weight residual
     110.42  115.72   -5.30 1.99e+00 2.53e-01 7.08e+00
  angle pdb=" N   LEU A 268 "
        pdb=" CA  LEU A 268 "
        pdb=" C   LEU A 268 "
      ideal   model   delta    sigma   weight residual
     109.81  115.67   -5.86 2.21e+00 2.05e-01 7.02e+00
  angle pdb=" C   GLN B 561 "
        pdb=" N   TRP B 562 "
        pdb=" CA  TRP B 562 "
      ideal   model   delta    sigma   weight residual
     121.80  126.80   -5.00 2.44e+00 1.68e-01 4.20e+00
  angle pdb=" N   ILE B 624 "
        pdb=" CA  ILE B 624 "
        pdb=" C   ILE B 624 "
      ideal   model   delta    sigma   weight residual
     112.35  109.50    2.85 1.41e+00 5.03e-01 4.09e+00
  angle pdb=" C   ILE B 451 "
        pdb=" N   CYS B 452 "
        pdb=" CA  CYS B 452 "
      ideal   model   delta    sigma   weight residual
     122.08  118.62    3.46 1.84e+00 2.95e-01 3.53e+00
  ... (remaining 7481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 2943
       17.13 -    34.27: 253
       34.27 -    51.40: 44
       51.40 -    68.53: 6
       68.53 -    85.66: 3
  Dihedral angle restraints: 3249
    sinusoidal: 1151
      harmonic: 2098
  Sorted by residual:
  dihedral pdb=" CB  CYS A 385 "
           pdb=" SG  CYS A 385 "
           pdb=" SG  CYS A 390 "
           pdb=" CB  CYS A 390 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.65   50.35     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CB  CYS A 245 "
           pdb=" SG  CYS A 245 "
           pdb=" SG  CYS A 261 "
           pdb=" CB  CYS A 261 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.91   45.09     1      1.00e+01 1.00e-02 2.82e+01
  dihedral pdb=" CA  LEU A 288 "
           pdb=" C   LEU A 288 "
           pdb=" N   GLU A 289 "
           pdb=" CA  GLU A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.28   17.72     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 3246 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 580
       0.034 -    0.068: 204
       0.068 -    0.102: 82
       0.102 -    0.135: 33
       0.135 -    0.169: 3
  Chirality restraints: 902
  Sorted by residual:
  chirality pdb=" CA  ILE A 830 "
            pdb=" N   ILE A 830 "
            pdb=" C   ILE A 830 "
            pdb=" CB  ILE A 830 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  ILE A 891 "
            pdb=" N   ILE A 891 "
            pdb=" C   ILE A 891 "
            pdb=" CB  ILE A 891 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  ILE A  91 "
            pdb=" N   ILE A  91 "
            pdb=" C   ILE A  91 "
            pdb=" CB  ILE A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.69e-01
  ... (remaining 899 not shown)

  Planarity restraints: 965
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 562 "    0.017 2.00e-02 2.50e+03   1.32e-02 4.36e+00
        pdb=" CG  TRP B 562 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 562 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 562 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 562 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 562 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 562 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 562 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 562 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 562 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 855 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.16e+00
        pdb=" N   PRO A 856 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 856 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 856 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 619 "   -0.011 2.00e-02 2.50e+03   8.73e-03 1.33e+00
        pdb=" CG  PHE B 619 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 619 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 619 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 619 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 619 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 619 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 962 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 237
        2.69 -     3.24: 6075
        3.24 -     3.80: 9493
        3.80 -     4.35: 11963
        4.35 -     4.90: 18465
  Nonbonded interactions: 46233
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 937 "
            pdb=" O   LEU A1001 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   ALA A 163 "
            pdb=" OH  TYR A 247 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" OG  SER A  60 "
            pdb=" OG1 THR A  74 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   SER B 470 "
            pdb=" NH1 ARG B 508 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   LEU A 268 "
            pdb=" OG  SER A 271 "
     model   vdw
     2.216 3.040
  ... (remaining 46228 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.770
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.560
  Find NCS groups from input model:        0.020
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
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      :  0.003   0.038   5481  Z= 0.130
  Angle     :  0.628   6.575   7499  Z= 0.328
  Chirality :  0.044   0.169    902
  Planarity :  0.003   0.037    964
  Dihedral  : 13.216  85.664   1874
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 25.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.32), residues: 706
  helix:  1.25 (0.69), residues: 76
  sheet: -1.26 (0.32), residues: 253
  loop : -2.19 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 574 
 TYR   0.012   0.001   TYR B 442 
 PHE   0.020   0.002   PHE B 619 
 TRP   0.036   0.002   TRP B 562 
 HIS   0.008   0.002   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5475)
  covalent geometry    : angle       0.62578 ( 7486)
  SS BOND              : bond        0.00150 (    5)
  SS BOND              : angle       1.34659 (   10)
  hydrogen bonds       : bond        0.17034 (  181)
  hydrogen bonds       : angle       8.48671 (  474)
  link_NAG-ASN         : bond        0.00132 (    1)
  link_NAG-ASN         : angle       1.82363 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0485
  time to fit residues: 2.1732
Evaluate side-chains
  25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN
A 902 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.034116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.026338 restraints weight = 67277.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.027214 restraints weight = 49636.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.027884 restraints weight = 39247.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.028407 restraints weight = 32619.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.028817 restraints weight = 28044.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5481  Z= 0.135
  Angle     :  0.599   6.251   7499  Z= 0.315
  Chirality :  0.043   0.150    902
  Planarity :  0.004   0.039    964
  Dihedral  :  5.203  18.055    775
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.31), residues: 706
  helix:  1.27 (0.67), residues: 79
  sheet: -1.37 (0.32), residues: 251
  loop : -2.30 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  50 
 TYR   0.034   0.002   TYR B 442 
 PHE   0.013   0.001   PHE A 831 
 TRP   0.024   0.002   TRP B 562 
 HIS   0.003   0.001   HIS A 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5475)
  covalent geometry    : angle       0.59657 ( 7486)
  SS BOND              : bond        0.00238 (    5)
  SS BOND              : angle       1.36317 (   10)
  hydrogen bonds       : bond        0.03823 (  181)
  hydrogen bonds       : angle       7.35614 (  474)
  link_NAG-ASN         : bond        0.00197 (    1)
  link_NAG-ASN         : angle       1.60976 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0583
  time to fit residues: 2.6078
Evaluate side-chains
  24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0670
   chunk 13 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 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 = 0.2903 r_free = 0.2903 target = 0.033622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.025856 restraints weight = 66748.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.026734 restraints weight = 49181.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.027408 restraints weight = 38811.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.027937 restraints weight = 32121.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.028352 restraints weight = 27536.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5481  Z= 0.150
  Angle     :  0.608   6.300   7499  Z= 0.317
  Chirality :  0.044   0.193    902
  Planarity :  0.004   0.040    964
  Dihedral  :  5.228  18.271    775
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.31), residues: 706
  helix:  1.29 (0.67), residues: 75
  sheet: -1.40 (0.32), residues: 252
  loop : -2.31 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 158 
 TYR   0.026   0.002   TYR B 442 
 PHE   0.013   0.002   PHE A 831 
 TRP   0.018   0.002   TRP B 562 
 HIS   0.003   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5475)
  covalent geometry    : angle       0.60081 ( 7486)
  SS BOND              : bond        0.00273 (    5)
  SS BOND              : angle       1.54107 (   10)
  hydrogen bonds       : bond        0.03326 (  181)
  hydrogen bonds       : angle       7.11404 (  474)
  link_NAG-ASN         : bond        0.00692 (    1)
  link_NAG-ASN         : angle       3.83083 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0580
  time to fit residues: 2.6162
Evaluate side-chains
  24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 70 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0670
   chunk 56 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.034337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.026510 restraints weight = 66489.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.027379 restraints weight = 49285.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.028049 restraints weight = 39215.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.028579 restraints weight = 32662.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.028994 restraints weight = 28183.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5481  Z= 0.111
  Angle     :  0.581   5.819   7499  Z= 0.301
  Chirality :  0.044   0.153    902
  Planarity :  0.003   0.040    964
  Dihedral  :  4.981  17.271    775
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.31), residues: 706
  helix:  1.23 (0.67), residues: 75
  sheet: -1.30 (0.32), residues: 258
  loop : -2.37 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 158 
 TYR   0.019   0.001   TYR B 442 
 PHE   0.015   0.001   PHE B 655 
 TRP   0.016   0.001   TRP B 562 
 HIS   0.003   0.001   HIS A 828 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 5475)
  covalent geometry    : angle       0.57766 ( 7486)
  SS BOND              : bond        0.00232 (    5)
  SS BOND              : angle       1.63548 (   10)
  hydrogen bonds       : bond        0.02794 (  181)
  hydrogen bonds       : angle       6.73264 (  474)
  link_NAG-ASN         : bond        0.00125 (    1)
  link_NAG-ASN         : angle       1.87382 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0590
  time to fit residues: 2.6549
Evaluate side-chains
  24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    0.0970
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.039620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.033243 restraints weight = 71728.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.034141 restraints weight = 46841.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.034808 restraints weight = 34113.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.035300 restraints weight = 26490.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.035611 restraints weight = 21626.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5481  Z= 0.116
  Angle     :  0.583   6.524   7499  Z= 0.300
  Chirality :  0.043   0.196    902
  Planarity :  0.003   0.041    964
  Dihedral  :  4.925  17.474    775
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.31), residues: 706
  helix:  1.24 (0.67), residues: 75
  sheet: -1.31 (0.32), residues: 255
  loop : -2.29 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 158 
 TYR   0.007   0.001   TYR B 489 
 PHE   0.018   0.001   PHE A 831 
 TRP   0.044   0.002   TRP B 562 
 HIS   0.003   0.001   HIS A 828 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5475)
  covalent geometry    : angle       0.57930 ( 7486)
  SS BOND              : bond        0.00258 (    5)
  SS BOND              : angle       1.60409 (   10)
  hydrogen bonds       : bond        0.02778 (  181)
  hydrogen bonds       : angle       6.66998 (  474)
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       1.59643 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  442 TYR cc_start: 0.8141 (m-80) cc_final: 0.7941 (m-80)
REVERT: B  450 MET cc_start: 0.8699 (pmm) cc_final: 0.7785 (pmm)
REVERT: B  585 ILE cc_start: 0.9381 (mp) cc_final: 0.8866 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0615
  time to fit residues: 2.6364
Evaluate side-chains
  25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 41 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0770
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.8742

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.033368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.025609 restraints weight = 68796.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.026469 restraints weight = 50772.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.027120 restraints weight = 40170.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.027627 restraints weight = 33456.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.028016 restraints weight = 28884.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5481  Z= 0.166
  Angle     :  0.604   6.677   7499  Z= 0.315
  Chirality :  0.043   0.172    902
  Planarity :  0.004   0.042    964
  Dihedral  :  5.050  19.176    775
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 19.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.37 (0.31), residues: 706
  helix:  1.15 (0.63), residues: 81
  sheet: -1.43 (0.32), residues: 259
  loop : -2.34 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 158 
 TYR   0.015   0.002   TYR B 442 
 PHE   0.015   0.002   PHE A 831 
 TRP   0.030   0.002   TRP B 562 
 HIS   0.002   0.001   HIS A 828 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5475)
  covalent geometry    : angle       0.60091 ( 7486)
  SS BOND              : bond        0.00304 (    5)
  SS BOND              : angle       1.56333 (   10)
  hydrogen bonds       : bond        0.03110 (  181)
  hydrogen bonds       : angle       6.74436 (  474)
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       1.74333 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  585 ILE cc_start: 0.9425 (mp) cc_final: 0.8949 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0569
  time to fit residues: 2.5522
Evaluate side-chains
  24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.032874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.025330 restraints weight = 69759.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.026161 restraints weight = 51544.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.026789 restraints weight = 40907.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.027284 restraints weight = 34062.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.027664 restraints weight = 29464.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5481  Z= 0.199
  Angle     :  0.668   9.734   7499  Z= 0.344
  Chirality :  0.044   0.217    902
  Planarity :  0.004   0.045    964
  Dihedral  :  5.361  20.525    775
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 24.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.45 (0.31), residues: 706
  helix:  1.13 (0.63), residues: 81
  sheet: -1.41 (0.32), residues: 260
  loop : -2.49 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 158 
 TYR   0.020   0.002   TYR B 442 
 PHE   0.018   0.002   PHE A 906 
 TRP   0.027   0.002   TRP B 562 
 HIS   0.002   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 5475)
  covalent geometry    : angle       0.65524 ( 7486)
  SS BOND              : bond        0.00380 (    5)
  SS BOND              : angle       1.49197 (   10)
  hydrogen bonds       : bond        0.03324 (  181)
  hydrogen bonds       : angle       7.01725 (  474)
  link_NAG-ASN         : bond        0.01642 (    1)
  link_NAG-ASN         : angle       6.05421 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  585 ILE cc_start: 0.9415 (mp) cc_final: 0.8927 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0566
  time to fit residues: 2.3703
Evaluate side-chains
  22 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 21 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:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.033296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.025807 restraints weight = 67859.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.026677 restraints weight = 49383.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.027338 restraints weight = 38699.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.027852 restraints weight = 31922.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.028256 restraints weight = 27374.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5481  Z= 0.175
  Angle     :  0.643   6.728   7499  Z= 0.333
  Chirality :  0.044   0.207    902
  Planarity :  0.004   0.044    964
  Dihedral  :  5.403  20.090    775
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 22.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.57 (0.31), residues: 706
  helix:  0.97 (0.62), residues: 81
  sheet: -1.53 (0.32), residues: 258
  loop : -2.50 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 158 
 TYR   0.020   0.002   TYR B 442 
 PHE   0.016   0.002   PHE A 831 
 TRP   0.023   0.002   TRP B 562 
 HIS   0.002   0.001   HIS A 828 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5475)
  covalent geometry    : angle       0.63707 ( 7486)
  SS BOND              : bond        0.00392 (    5)
  SS BOND              : angle       1.51628 (   10)
  hydrogen bonds       : bond        0.03168 (  181)
  hydrogen bonds       : angle       7.01237 (  474)
  link_NAG-ASN         : bond        0.00443 (    1)
  link_NAG-ASN         : angle       3.68234 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  585 ILE cc_start: 0.9411 (mp) cc_final: 0.8901 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0566
  time to fit residues: 2.6029
Evaluate side-chains
  23 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 17 optimal weight:    0.1980
   chunk 28 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.033433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.025783 restraints weight = 68599.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.026637 restraints weight = 50498.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.027172 restraints weight = 40028.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.027748 restraints weight = 33842.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.028149 restraints weight = 29108.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5481  Z= 0.146
  Angle     :  0.622   6.584   7499  Z= 0.319
  Chirality :  0.044   0.188    902
  Planarity :  0.004   0.043    964
  Dihedral  :  5.292  19.056    775
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 20.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.31), residues: 706
  helix:  0.92 (0.62), residues: 81
  sheet: -1.49 (0.32), residues: 249
  loop : -2.46 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 158 
 TYR   0.017   0.002   TYR B 442 
 PHE   0.015   0.002   PHE A 831 
 TRP   0.024   0.002   TRP B 562 
 HIS   0.002   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5475)
  covalent geometry    : angle       0.61761 ( 7486)
  SS BOND              : bond        0.00305 (    5)
  SS BOND              : angle       1.52521 (   10)
  hydrogen bonds       : bond        0.02916 (  181)
  hydrogen bonds       : angle       6.92208 (  474)
  link_NAG-ASN         : bond        0.00423 (    1)
  link_NAG-ASN         : angle       2.91308 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  585 ILE cc_start: 0.9410 (mp) cc_final: 0.8932 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0622
  time to fit residues: 2.5097
Evaluate side-chains
  23 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0770
   chunk 14 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.033655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.025931 restraints weight = 68186.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.026797 restraints weight = 50076.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.027453 restraints weight = 39551.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.027969 restraints weight = 32861.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.028367 restraints weight = 28330.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5481  Z= 0.139
  Angle     :  0.616   6.548   7499  Z= 0.315
  Chirality :  0.044   0.190    902
  Planarity :  0.004   0.041    964
  Dihedral  :  5.244  18.869    775
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 20.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.49 (0.31), residues: 706
  helix:  0.97 (0.62), residues: 81
  sheet: -1.45 (0.33), residues: 249
  loop : -2.45 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 158 
 TYR   0.016   0.002   TYR B 442 
 PHE   0.015   0.002   PHE A 831 
 TRP   0.023   0.002   TRP B 562 
 HIS   0.002   0.001   HIS A 828 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5475)
  covalent geometry    : angle       0.61216 ( 7486)
  SS BOND              : bond        0.00282 (    5)
  SS BOND              : angle       1.45420 (   10)
  hydrogen bonds       : bond        0.02831 (  181)
  hydrogen bonds       : angle       6.85102 (  474)
  link_NAG-ASN         : bond        0.00340 (    1)
  link_NAG-ASN         : angle       2.66719 (    3)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  585 ILE cc_start: 0.9408 (mp) cc_final: 0.8932 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0576
  time to fit residues: 2.5265
Evaluate side-chains
  25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN
B 548 ASN
B 665 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.032606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.025223 restraints weight = 71006.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.026050 restraints weight = 52234.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.026666 restraints weight = 41343.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.027161 restraints weight = 34396.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.027542 restraints weight = 29591.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5481  Z= 0.218
  Angle     :  0.676   6.863   7499  Z= 0.353
  Chirality :  0.045   0.170    902
  Planarity :  0.004   0.044    964
  Dihedral  :  5.606  21.266    775
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 27.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.30), residues: 706
  helix:  0.58 (0.59), residues: 85
  sheet: -1.62 (0.32), residues: 241
  loop : -2.66 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 158 
 TYR   0.026   0.002   TYR B 442 
 PHE   0.017   0.002   PHE A 831 
 TRP   0.021   0.003   TRP B 562 
 HIS   0.003   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 5475)
  covalent geometry    : angle       0.67153 ( 7486)
  SS BOND              : bond        0.00400 (    5)
  SS BOND              : angle       1.44821 (   10)
  hydrogen bonds       : bond        0.03463 (  181)
  hydrogen bonds       : angle       7.19121 (  474)
  link_NAG-ASN         : bond        0.00494 (    1)
  link_NAG-ASN         : angle       2.91342 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1007.93 seconds
wall clock time: 18 minutes 8.13 seconds (1088.13 seconds total)