Starting phenix.real_space_refine
on Fri Oct 10 10:42:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k45_22660/10_2025/7k45_22660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k45_22660/10_2025/7k45_22660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k45_22660/10_2025/7k45_22660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k45_22660/10_2025/7k45_22660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k45_22660/10_2025/7k45_22660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k45_22660/10_2025/7k45_22660.cif"
  }
  resolution = 3.7
  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=   0.015
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      16      5.16       5
     C    1960      2.51       5
     N     529      2.21       5
     O     533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3038
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 849
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "L"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 730
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 1431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1431
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 135
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.14, per 1000 atoms: 0.38
  Number of scatterers: 3038
  At special positions: 0
  Unit cell: (70.35, 55.65, 100.8, 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      16     16.00
     O     533      8.00
     N     529      7.00
     C    1960      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 106 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN B 343 "
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 124.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  764

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 10 sheets defined
      15.3% alpha, 33.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 31
    Processing helix  chain 'H' and resid 64 through 66
      No H-bonds generated for 'chain 'H' and resid 64 through 66'
    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 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.745A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.815A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.227A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.295A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.052A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.738A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474

    126 hydrogen bonds defined for protein.
    285 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: 0.45

  Time building geometry restraints manager: 0.39 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.33: 933
        1.33 -     1.47: 940
        1.47 -     1.60: 1225
        1.60 -     1.73: 2
        1.73 -     1.86: 18
  Bond restraints: 3118
  Sorted by residual:
  bond pdb=" CB  ILE L   2 "
       pdb=" CG1 ILE L   2 "
    ideal  model  delta    sigma   weight residual
    1.530  1.611 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" C5  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.479 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" C5  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.474 -0.061 2.00e-02 2.50e+03 9.37e+00
  bond pdb=" NE1 TRP H  50 "
       pdb=" CE2 TRP H  50 "
    ideal  model  delta    sigma   weight residual
    1.370  1.337  0.033 1.10e-02 8.26e+03 8.78e+00
  bond pdb=" CB  ASN B 422 "
       pdb=" CG  ASN B 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.446  0.070 2.50e-02 1.60e+03 7.94e+00
  ... (remaining 3113 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 3463
        1.63 -     3.26: 641
        3.26 -     4.89: 116
        4.89 -     6.53: 36
        6.53 -     8.16: 11
  Bond angle restraints: 4267
  Sorted by residual:
  angle pdb=" C   GLY H   8 "
        pdb=" N   PRO H   9 "
        pdb=" CA  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     120.03  128.19   -8.16 9.90e-01 1.02e+00 6.79e+01
  angle pdb=" C   ILE L  59 "
        pdb=" N   PRO L  60 "
        pdb=" CA  PRO L  60 "
      ideal   model   delta    sigma   weight residual
     120.21  126.95   -6.74 9.60e-01 1.09e+00 4.93e+01
  angle pdb=" C   SER B 383 "
        pdb=" N   PRO B 384 "
        pdb=" CA  PRO B 384 "
      ideal   model   delta    sigma   weight residual
     119.56  126.42   -6.86 1.02e+00 9.61e-01 4.53e+01
  angle pdb=" C   ALA B 520 "
        pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
      ideal   model   delta    sigma   weight residual
     119.56  126.33   -6.77 1.02e+00 9.61e-01 4.41e+01
  angle pdb=" C   GLN B 498 "
        pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     119.87  126.70   -6.83 1.04e+00 9.25e-01 4.31e+01
  ... (remaining 4262 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 1752
       16.65 -    33.30: 55
       33.30 -    49.94: 10
       49.94 -    66.59: 4
       66.59 -    83.24: 1
  Dihedral angle restraints: 1822
    sinusoidal: 618
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  121.87  -28.87     1      1.00e+01 1.00e-02 1.19e+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   66.25   26.75     1      1.00e+01 1.00e-02 1.03e+01
  dihedral pdb=" C   TYR L  92 "
           pdb=" N   TYR L  92 "
           pdb=" CA  TYR L  92 "
           pdb=" CB  TYR L  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -115.16   -7.44     0      2.50e+00 1.60e-01 8.85e+00
  ... (remaining 1819 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 306
       0.068 -    0.136: 127
       0.136 -    0.204: 28
       0.204 -    0.272: 5
       0.272 -    0.340: 4
  Chirality restraints: 470
  Sorted by residual:
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.64e+01
  chirality pdb=" C2  NAG A   2 "
            pdb=" C1  NAG A   2 "
            pdb=" C3  NAG A   2 "
            pdb=" N2  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" C2  NAG A   1 "
            pdb=" C1  NAG A   1 "
            pdb=" C3  NAG A   1 "
            pdb=" N2  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.33 2.00e-01 2.50e+01 2.65e+00
  ... (remaining 467 not shown)

  Planarity restraints: 561
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  92 "   -0.030 2.00e-02 2.50e+03   1.51e-02 4.56e+00
        pdb=" CG  TYR L  92 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  92 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  92 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  92 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  92 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  92 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR L  92 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  50 "    0.027 2.00e-02 2.50e+03   1.34e-02 4.49e+00
        pdb=" CG  TRP H  50 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  50 "   -0.019 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  50 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  50 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  50 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  50 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  50 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "   -0.023 2.00e-02 2.50e+03   1.32e-02 4.34e+00
        pdb=" CG  TRP H  47 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "    0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 558 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.03: 1766
        3.03 -     3.50: 2712
        3.50 -     3.97: 4880
        3.97 -     4.43: 5575
        4.43 -     4.90: 9162
  Nonbonded interactions: 24095
  Sorted by model distance:
  nonbonded pdb=" N   LYS B 462 "
            pdb=" O   LYS B 462 "
     model   vdw
     2.568 2.496
  nonbonded pdb=" N   GLU L  80 "
            pdb=" O   GLU L  80 "
     model   vdw
     2.592 2.496
  nonbonded pdb=" CB  GLN H   6 "
            pdb=" OE1 GLN H   6 "
     model   vdw
     2.598 2.752
  nonbonded pdb=" N   GLY B 502 "
            pdb=" O   GLY B 502 "
     model   vdw
     2.601 2.496
  nonbonded pdb=" N   SER B 373 "
            pdb=" N   PHE B 374 "
     model   vdw
     2.605 2.560
  ... (remaining 24090 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:             8.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.440
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
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      :  0.015   0.092   3127  Z= 0.793
  Angle     :  1.425   8.157   4287  Z= 0.964
  Chirality :  0.079   0.340    470
  Planarity :  0.006   0.039    560
  Dihedral  :  9.350  83.236   1037
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.41), residues: 411
  helix: -4.00 (0.49), residues: 33
  sheet:  1.14 (0.43), residues: 150
  loop :  1.17 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  67 
 TYR   0.030   0.004   TYR L  92 
 PHE   0.013   0.003   PHE H  64 
 TRP   0.027   0.008   TRP H  50 
 HIS   0.002   0.001   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.01446 ( 3118)
  covalent geometry    : angle       1.41601 ( 4267)
  SS BOND              : bond        0.02869 (    7)
  SS BOND              : angle       2.53855 (   14)
  hydrogen bonds       : bond        0.15086 (  116)
  hydrogen bonds       : angle       9.13726 (  285)
  link_BETA1-4         : bond        0.06505 (    1)
  link_BETA1-4         : angle       4.01691 (    3)
  link_NAG-ASN         : bond        0.06242 (    1)
  link_NAG-ASN         : angle       1.79789 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.7080 (t80) cc_final: 0.6653 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1028
  time to fit residues: 9.7635
Evaluate side-chains
  44 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0770
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    0.1980
   chunk 19 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0470
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.0994

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.106038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.096058 restraints weight = 7321.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.098743 restraints weight = 3961.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.100564 restraints weight = 2485.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.101793 restraints weight = 1705.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.102661 restraints weight = 1254.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3127  Z= 0.136
  Angle     :  0.666   8.586   4287  Z= 0.350
  Chirality :  0.048   0.141    470
  Planarity :  0.005   0.036    560
  Dihedral  :  4.888  22.717    502
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 13.77 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.41), residues: 411
  helix: -3.56 (0.69), residues: 27
  sheet:  0.71 (0.41), residues: 150
  loop :  0.91 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  24 
 TYR   0.022   0.002   TYR L  92 
 PHE   0.013   0.002   PHE B 497 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.002   0.002   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3118)
  covalent geometry    : angle       0.64050 ( 4267)
  SS BOND              : bond        0.00870 (    7)
  SS BOND              : angle       3.14043 (   14)
  hydrogen bonds       : bond        0.03725 (  116)
  hydrogen bonds       : angle       6.76232 (  285)
  link_BETA1-4         : bond        0.00786 (    1)
  link_BETA1-4         : angle       1.74351 (    3)
  link_NAG-ASN         : bond        0.00294 (    1)
  link_NAG-ASN         : angle       0.59223 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   37 TYR cc_start: 0.8576 (m-10) cc_final: 0.7974 (m-80)
REVERT: B  398 ASP cc_start: 0.8390 (m-30) cc_final: 0.7957 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0778
  time to fit residues: 5.9273
Evaluate side-chains
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  442 ASP
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 10 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 27 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:
H   6 GLN
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.099076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.088906 restraints weight = 7477.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.091535 restraints weight = 4074.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.093317 restraints weight = 2572.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.094476 restraints weight = 1785.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.095383 restraints weight = 1337.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   3127  Z= 0.247
  Angle     :  0.689   8.413   4287  Z= 0.371
  Chirality :  0.048   0.139    470
  Planarity :  0.005   0.036    560
  Dihedral  :  5.037  26.098    502
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 12.96 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.39), residues: 411
  helix: -3.07 (1.00), residues: 20
  sheet:  0.30 (0.40), residues: 152
  loop :  0.54 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  24 
 TYR   0.044   0.002   TYR L  92 
 PHE   0.012   0.002   PHE B 347 
 TRP   0.016   0.002   TRP L  36 
 HIS   0.005   0.003   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 ( 3118)
  covalent geometry    : angle       0.67229 ( 4267)
  SS BOND              : bond        0.00297 (    7)
  SS BOND              : angle       2.59548 (   14)
  hydrogen bonds       : bond        0.04166 (  116)
  hydrogen bonds       : angle       6.35565 (  285)
  link_BETA1-4         : bond        0.00393 (    1)
  link_BETA1-4         : angle       1.86542 (    3)
  link_NAG-ASN         : bond        0.00369 (    1)
  link_NAG-ASN         : angle       0.51534 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7667 (m-30) cc_final: 0.7442 (m-30)
REVERT: B  369 TYR cc_start: 0.7046 (t80) cc_final: 0.6745 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0804
  time to fit residues: 5.2082
Evaluate side-chains
  52 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0770
   chunk 9 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 0 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0770
   chunk 1 optimal weight:    0.4980
   chunk 21 optimal weight:    0.1980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.2096

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.100582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.090872 restraints weight = 7223.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.093386 restraints weight = 4082.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.095082 restraints weight = 2638.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.096296 restraints weight = 1861.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.097096 restraints weight = 1389.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3127  Z= 0.149
  Angle     :  0.636   7.628   4287  Z= 0.340
  Chirality :  0.047   0.134    470
  Planarity :  0.004   0.036    560
  Dihedral  :  4.843  25.029    502
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 14.98 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.39), residues: 411
  helix: -2.86 (1.08), residues: 20
  sheet:  0.28 (0.39), residues: 148
  loop :  0.48 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  55 
 TYR   0.032   0.001   TYR L  92 
 PHE   0.008   0.001   PHE H  27 
 TRP   0.010   0.001   TRP B 436 
 HIS   0.003   0.002   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3118)
  covalent geometry    : angle       0.61868 ( 4267)
  SS BOND              : bond        0.00285 (    7)
  SS BOND              : angle       2.59607 (   14)
  hydrogen bonds       : bond        0.03619 (  116)
  hydrogen bonds       : angle       6.07812 (  285)
  link_BETA1-4         : bond        0.00560 (    1)
  link_BETA1-4         : angle       1.45214 (    3)
  link_NAG-ASN         : bond        0.00316 (    1)
  link_NAG-ASN         : angle       0.28083 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.7083 (t80) cc_final: 0.6623 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0925
  time to fit residues: 5.9740
Evaluate side-chains
  51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.0040
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0570
   chunk 16 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.3110

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.098778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.089148 restraints weight = 7291.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091557 restraints weight = 4096.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.093206 restraints weight = 2660.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.094382 restraints weight = 1886.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.095122 restraints weight = 1422.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3127  Z= 0.183
  Angle     :  0.633   7.577   4287  Z= 0.335
  Chirality :  0.047   0.136    470
  Planarity :  0.005   0.048    560
  Dihedral  :  4.792  22.788    502
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 14.98 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.40), residues: 411
  helix: -3.37 (0.83), residues: 27
  sheet:  0.04 (0.39), residues: 155
  loop :  0.76 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  55 
 TYR   0.034   0.002   TYR L  92 
 PHE   0.008   0.001   PHE H  27 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.003   0.002   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 3118)
  covalent geometry    : angle       0.62462 ( 4267)
  SS BOND              : bond        0.00276 (    7)
  SS BOND              : angle       1.81804 (   14)
  hydrogen bonds       : bond        0.03600 (  116)
  hydrogen bonds       : angle       6.01319 (  285)
  link_BETA1-4         : bond        0.00369 (    1)
  link_BETA1-4         : angle       1.46350 (    3)
  link_NAG-ASN         : bond        0.00288 (    1)
  link_NAG-ASN         : angle       0.33519 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.7149 (t80) cc_final: 0.6619 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 58
  average time/residue: 0.0885
  time to fit residues: 6.0119
Evaluate side-chains
  53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.095835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.085934 restraints weight = 7425.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.088325 restraints weight = 4261.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.089972 restraints weight = 2809.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.091136 restraints weight = 2013.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.091860 restraints weight = 1530.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   3127  Z= 0.280
  Angle     :  0.706   7.369   4287  Z= 0.376
  Chirality :  0.048   0.134    470
  Planarity :  0.005   0.045    560
  Dihedral  :  5.229  27.824    502
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 13.36 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.40), residues: 411
  helix: -2.99 (1.05), residues: 20
  sheet:  0.05 (0.40), residues: 152
  loop :  0.17 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  55 
 TYR   0.039   0.002   TYR L  92 
 PHE   0.022   0.002   PHE B 392 
 TRP   0.016   0.002   TRP L  36 
 HIS   0.006   0.004   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 ( 3118)
  covalent geometry    : angle       0.70213 ( 4267)
  SS BOND              : bond        0.00448 (    7)
  SS BOND              : angle       1.38302 (   14)
  hydrogen bonds       : bond        0.04095 (  116)
  hydrogen bonds       : angle       6.21497 (  285)
  link_BETA1-4         : bond        0.00506 (    1)
  link_BETA1-4         : angle       1.57945 (    3)
  link_NAG-ASN         : bond        0.00226 (    1)
  link_NAG-ASN         : angle       0.40951 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: L  102 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7110 (mp10)
REVERT: B  369 TYR cc_start: 0.7159 (t80) cc_final: 0.6560 (t80)
REVERT: B  430 THR cc_start: 0.8196 (m) cc_final: 0.7996 (p)
  outliers start: 14
  outliers final: 11
  residues processed: 52
  average time/residue: 0.0806
  time to fit residues: 4.9635
Evaluate side-chains
  51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.0770
   chunk 1 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0870
   chunk 23 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.2116

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.098744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.088945 restraints weight = 7442.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.091386 restraints weight = 4226.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.093038 restraints weight = 2751.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.094107 restraints weight = 1959.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.094943 restraints weight = 1507.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3127  Z= 0.142
  Angle     :  0.608   6.770   4287  Z= 0.320
  Chirality :  0.046   0.139    470
  Planarity :  0.005   0.040    560
  Dihedral  :  4.862  29.345    502
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 16.19 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.41), residues: 411
  helix: -2.91 (1.04), residues: 20
  sheet:  0.11 (0.40), residues: 149
  loop :  0.18 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  55 
 TYR   0.030   0.002   TYR L  92 
 PHE   0.013   0.001   PHE B 392 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.003   0.002   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3118)
  covalent geometry    : angle       0.60472 ( 4267)
  SS BOND              : bond        0.00366 (    7)
  SS BOND              : angle       1.20390 (   14)
  hydrogen bonds       : bond        0.03451 (  116)
  hydrogen bonds       : angle       6.07224 (  285)
  link_BETA1-4         : bond        0.00689 (    1)
  link_BETA1-4         : angle       1.26331 (    3)
  link_NAG-ASN         : bond        0.00310 (    1)
  link_NAG-ASN         : angle       0.24939 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: L  102 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.6821 (mp10)
  outliers start: 12
  outliers final: 10
  residues processed: 51
  average time/residue: 0.0837
  time to fit residues: 4.9347
Evaluate side-chains
  49 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0870
   chunk 19 optimal weight:    0.2980
   chunk 13 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0060
   overall best weight:    0.1974

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.099444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.089616 restraints weight = 7378.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.092092 restraints weight = 4201.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.093763 restraints weight = 2728.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.094861 restraints weight = 1940.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.095680 restraints weight = 1477.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.4737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3127  Z= 0.137
  Angle     :  0.599   7.761   4287  Z= 0.314
  Chirality :  0.045   0.139    470
  Planarity :  0.005   0.040    560
  Dihedral  :  4.700  29.824    502
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 15.79 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.41), residues: 411
  helix: -2.90 (1.04), residues: 20
  sheet:  0.03 (0.40), residues: 152
  loop :  0.25 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 408 
 TYR   0.028   0.001   TYR L  92 
 PHE   0.011   0.001   PHE B 392 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.002   0.001   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3118)
  covalent geometry    : angle       0.59588 ( 4267)
  SS BOND              : bond        0.00350 (    7)
  SS BOND              : angle       1.06339 (   14)
  hydrogen bonds       : bond        0.03280 (  116)
  hydrogen bonds       : angle       5.94612 (  285)
  link_BETA1-4         : bond        0.00482 (    1)
  link_BETA1-4         : angle       1.21293 (    3)
  link_NAG-ASN         : bond        0.00267 (    1)
  link_NAG-ASN         : angle       0.31626 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: L  102 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.6810 (mp10)
  outliers start: 13
  outliers final: 11
  residues processed: 51
  average time/residue: 0.0858
  time to fit residues: 5.0575
Evaluate side-chains
  51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.0000
   chunk 32 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0060
   chunk 10 optimal weight:    0.0570
   chunk 20 optimal weight:    0.3980
   chunk 34 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0980
   chunk 37 optimal weight:    0.3980
   chunk 21 optimal weight:    0.1980
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.0718

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.101561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.091718 restraints weight = 7321.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.094220 restraints weight = 4133.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.095828 restraints weight = 2684.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.097016 restraints weight = 1927.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.097801 restraints weight = 1449.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3127  Z= 0.106
  Angle     :  0.584   7.519   4287  Z= 0.304
  Chirality :  0.045   0.144    470
  Planarity :  0.004   0.038    560
  Dihedral  :  4.456  29.076    502
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.00 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.41), residues: 411
  helix: -2.78 (1.06), residues: 20
  sheet:  0.07 (0.40), residues: 152
  loop :  0.35 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 408 
 TYR   0.023   0.001   TYR L  92 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.000   0.000   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3118)
  covalent geometry    : angle       0.58174 ( 4267)
  SS BOND              : bond        0.00342 (    7)
  SS BOND              : angle       1.02270 (   14)
  hydrogen bonds       : bond        0.03093 (  116)
  hydrogen bonds       : angle       5.91660 (  285)
  link_BETA1-4         : bond        0.00471 (    1)
  link_BETA1-4         : angle       1.13324 (    3)
  link_NAG-ASN         : bond        0.00302 (    1)
  link_NAG-ASN         : angle       0.33057 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: L  102 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.6778 (mp10)
REVERT: B  408 ARG cc_start: 0.7146 (ttp80) cc_final: 0.6834 (tmt-80)
  outliers start: 10
  outliers final: 6
  residues processed: 49
  average time/residue: 0.0753
  time to fit residues: 4.3696
Evaluate side-chains
  43 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 3 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.1980
   chunk 5 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0670
   chunk 14 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0870
   chunk 23 optimal weight:    0.0370
   overall best weight:    0.0752

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
L  39 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.102810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.092975 restraints weight = 7214.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.095465 restraints weight = 4065.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.097164 restraints weight = 2637.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.098293 restraints weight = 1863.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.099112 restraints weight = 1406.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.5018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3127  Z= 0.104
  Angle     :  0.575   7.878   4287  Z= 0.300
  Chirality :  0.045   0.142    470
  Planarity :  0.004   0.038    560
  Dihedral  :  4.210  27.286    502
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.03 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.42), residues: 411
  helix: -2.61 (1.44), residues: 12
  sheet:  0.32 (0.41), residues: 153
  loop :  0.38 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 408 
 TYR   0.021   0.001   TYR L  92 
 PHE   0.008   0.001   PHE H  27 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.000   0.000   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3118)
  covalent geometry    : angle       0.57327 ( 4267)
  SS BOND              : bond        0.00289 (    7)
  SS BOND              : angle       0.88717 (   14)
  hydrogen bonds       : bond        0.02943 (  116)
  hydrogen bonds       : angle       5.76634 (  285)
  link_BETA1-4         : bond        0.00348 (    1)
  link_BETA1-4         : angle       1.12294 (    3)
  link_NAG-ASN         : bond        0.00275 (    1)
  link_NAG-ASN         : angle       0.39958 (    3)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: H  100 TYR cc_start: 0.7643 (t80) cc_final: 0.7405 (t80)
REVERT: L   37 TYR cc_start: 0.8719 (m-10) cc_final: 0.8092 (m-80)
REVERT: L  102 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.6698 (mp10)
  outliers start: 7
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0812
  time to fit residues: 4.3330
Evaluate side-chains
  45 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 23 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    0.1980
   chunk 29 optimal weight:    0.0670
   chunk 14 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0970
   overall best weight:    0.2716

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.099645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.090040 restraints weight = 7275.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.092419 restraints weight = 4250.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.093991 restraints weight = 2802.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.095043 restraints weight = 2018.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.095879 restraints weight = 1548.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3127  Z= 0.164
  Angle     :  0.607   7.632   4287  Z= 0.322
  Chirality :  0.045   0.135    470
  Planarity :  0.005   0.049    560
  Dihedral  :  4.520  28.559    502
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.03 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.42), residues: 411
  helix: -2.60 (1.50), residues: 12
  sheet:  0.28 (0.41), residues: 153
  loop :  0.35 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  24 
 TYR   0.025   0.002   TYR L  92 
 PHE   0.009   0.001   PHE B 392 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.002   0.001   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3118)
  covalent geometry    : angle       0.60504 ( 4267)
  SS BOND              : bond        0.00372 (    7)
  SS BOND              : angle       0.97605 (   14)
  hydrogen bonds       : bond        0.03407 (  116)
  hydrogen bonds       : angle       5.96092 (  285)
  link_BETA1-4         : bond        0.00316 (    1)
  link_BETA1-4         : angle       1.20368 (    3)
  link_NAG-ASN         : bond        0.00231 (    1)
  link_NAG-ASN         : angle       0.52217 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 895.27 seconds
wall clock time: 16 minutes 1.18 seconds (961.18 seconds total)