Starting phenix.real_space_refine
on Tue Feb 11 08:53:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mjl_23877/02_2025/7mjl_23877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mjl_23877/02_2025/7mjl_23877.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mjl_23877/02_2025/7mjl_23877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mjl_23877/02_2025/7mjl_23877.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mjl_23877/02_2025/7mjl_23877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mjl_23877/02_2025/7mjl_23877.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
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      19      5.16       5
     C    3037      2.51       5
     N     793      2.21       5
     O     939      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4788
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1564
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 11, 'TRANS': 185}
    Chain: "H"
      Number of atoms: 1585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1585
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1625
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200}
    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: 4.16, per 1000 atoms: 0.87
  Number of scatterers: 4788
  At special positions: 0
  Unit cell: (75, 62, 129, 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      19     16.00
     O     939      8.00
     N     793      7.00
     C    3037      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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 A1301 " - " ASN A 343 "
  Time building additional restraints: 1.74
  Conformation dependent library (CDL) restraints added in 617.2 milliseconds
  

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 14 sheets defined
      9.5% alpha, 42.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.873A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 384 through 389
      removed outlier: 4.098A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.697A  pdb=" N   ASN H  32 " --> pdb=" O   VAL H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.734A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.652A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL L  83 " --> pdb=" O   ALA L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing helix  chain 'L' and resid 121 through 126
      removed outlier: 3.641A  pdb=" N   LYS L 126 " --> pdb=" O   ASP L 122 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.613A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.594A  pdb=" N   THR H  77 " --> pdb=" O   HIS H  72 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.318A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.921A  pdb=" N   TYR H 106 " --> pdb=" O   ARG H  97 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.135A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.135A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.055A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS H 213 " --> pdb=" O   CYS H 200 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.632A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.390A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.390A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.437A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 145 through 150

    181 hydrogen bonds defined for protein.
    453 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 2.01 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: 1500
        1.34 -     1.46: 1168
        1.46 -     1.58: 2219
        1.58 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 4909
  Sorted by residual:
  bond pdb=" N   ASP H 101 "
       pdb=" CA  ASP H 101 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 5.98e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.60e+00
  bond pdb=" C   LYS H 205 "
       pdb=" N   PRO H 206 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.20e-02 6.94e+03 2.59e+00
  bond pdb=" CB  ASN H  73 "
       pdb=" CG  ASN H  73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.552 -0.036 2.50e-02 1.60e+03 2.05e+00
  bond pdb=" C   SER L  94 "
       pdb=" N   PRO L  95 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.032 2.34e-02 1.83e+03 1.87e+00
  ... (remaining 4904 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 6337
        1.67 -     3.33: 284
        3.33 -     5.00: 44
        5.00 -     6.66: 11
        6.66 -     8.33: 6
  Bond angle restraints: 6682
  Sorted by residual:
  angle pdb=" C   GLY H 100 "
        pdb=" N   ASP H 101 "
        pdb=" CA  ASP H 101 "
      ideal   model   delta    sigma   weight residual
     121.54  129.87   -8.33 1.91e+00 2.74e-01 1.90e+01
  angle pdb=" C   TRP L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" C   PHE A 515 "
        pdb=" N   GLU A 516 "
        pdb=" CA  GLU A 516 "
      ideal   model   delta    sigma   weight residual
     122.94  117.62    5.32 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" CA  ASP H 101 "
        pdb=" CB  ASP H 101 "
        pdb=" CG  ASP H 101 "
      ideal   model   delta    sigma   weight residual
     112.60  115.97   -3.37 1.00e+00 1.00e+00 1.14e+01
  angle pdb=" CA  LYS H 210 "
        pdb=" CB  LYS H 210 "
        pdb=" CG  LYS H 210 "
      ideal   model   delta    sigma   weight residual
     114.10  120.52   -6.42 2.00e+00 2.50e-01 1.03e+01
  ... (remaining 6677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.53: 2713
       16.53 -    33.06: 151
       33.06 -    49.59: 38
       49.59 -    66.12: 11
       66.12 -    82.65: 8
  Dihedral angle restraints: 2921
    sinusoidal: 1124
      harmonic: 1797
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.49  -74.49     1      1.00e+01 1.00e-02 7.03e+01
  dihedral pdb=" CB  CYS H 144 "
           pdb=" SG  CYS H 144 "
           pdb=" SG  CYS H 200 "
           pdb=" CB  CYS H 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.05  -51.05     1      1.00e+01 1.00e-02 3.56e+01
  dihedral pdb=" CA  HIS H  72 "
           pdb=" C   HIS H  72 "
           pdb=" N   ASN H  73 "
           pdb=" CA  ASN H  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.47  -22.53     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 2918 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 506
       0.047 -    0.094: 159
       0.094 -    0.142: 61
       0.142 -    0.189: 9
       0.189 -    0.236: 2
  Chirality restraints: 737
  Sorted by residual:
  chirality pdb=" CA  ASP H 101 "
            pdb=" N   ASP H 101 "
            pdb=" C   ASP H 101 "
            pdb=" CB  ASP H 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  ILE A 332 "
            pdb=" CA  ILE A 332 "
            pdb=" CG1 ILE A 332 "
            pdb=" CG2 ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  ILE L 117 "
            pdb=" CA  ILE L 117 "
            pdb=" CG1 ILE L 117 "
            pdb=" CG2 ILE L 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.17e-01
  ... (remaining 734 not shown)

  Planarity restraints: 859
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 478 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO A 479 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 479 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 479 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 152 "   -0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO H 153 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO H 153 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO H 153 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP L  60 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.47e+00
        pdb=" CG  ASP L  60 "   -0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASP L  60 "    0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP L  60 "    0.011 2.00e-02 2.50e+03
  ... (remaining 856 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1635
        2.86 -     3.37: 3870
        3.37 -     3.88: 8010
        3.88 -     4.39: 9038
        4.39 -     4.90: 15985
  Nonbonded interactions: 38538
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 353 "
            pdb=" NH1 ARG A 466 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" OG  SER A 366 "
            pdb=" OD1 ASN A 388 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" OD2 ASP A 420 "
            pdb=" OG  SER H  56 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OH  TYR A 453 "
            pdb=" OH  TYR H 102 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" OG  SER H 207 "
            pdb=" OG1 THR H 209 "
     model   vdw
     2.404 3.040
  ... (remaining 38533 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.120
  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:          0.000
  Check model and map are aligned:         1.920
  Set scattering table:                    0.000
  Process input model:                     16.190
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:18.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
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      :  0.005   0.046   4909  Z= 0.325
  Angle     :  0.818   8.326   6682  Z= 0.444
  Chirality :  0.054   0.236    737
  Planarity :  0.006   0.055    858
  Dihedral  : 12.247  82.651   1757
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.32), residues: 613
  helix: -4.72 (0.22), residues: 37
  sheet:  0.46 (0.32), residues: 243
  loop : -0.82 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.005   0.002   HIS H  72 
 PHE   0.015   0.002   PHE L  71 
 TYR   0.025   0.002   TYR A 495 
 ARG   0.006   0.001   ARG H  19 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLU cc_start: 0.8034 (pp20) cc_final: 0.7555 (pp20)
REVERT: A  528 LYS cc_start: 0.5794 (tttm) cc_final: 0.4720 (pptt)
REVERT: L  158 ASN cc_start: 0.7795 (m110) cc_final: 0.7591 (m110)
REVERT: L  167 ASP cc_start: 0.8609 (t0) cc_final: 0.8273 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 1.4340
  time to fit residues: 133.4794
Evaluate side-chains
  61 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0670
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0270
   chunk 29 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
H 201 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.065525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.054844 restraints weight = 12328.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.88
r_work: 0.2781 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4909  Z= 0.158
  Angle     :  0.531   6.643   6682  Z= 0.277
  Chirality :  0.043   0.138    737
  Planarity :  0.005   0.055    858
  Dihedral  :  4.852  36.343    699
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  9.23 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.33), residues: 613
  helix: -4.70 (0.49), residues: 20
  sheet:  0.65 (0.33), residues: 244
  loop : -0.36 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  72 
 PHE   0.006   0.001   PHE L  71 
 TYR   0.013   0.001   TYR A 495 
 ARG   0.010   0.001   ARG L  24 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9171 (m-30) cc_final: 0.8801 (m-30)
REVERT: A  516 GLU cc_start: 0.8103 (pp20) cc_final: 0.7649 (pp20)
REVERT: A  528 LYS cc_start: 0.6278 (tttm) cc_final: 0.4892 (pptt)
REVERT: H    3 GLN cc_start: 0.8285 (mm110) cc_final: 0.8049 (mm110)
REVERT: H   88 GLU cc_start: 0.9035 (pm20) cc_final: 0.8800 (pm20)
REVERT: L   17 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8216 (mt-10)
REVERT: L  158 ASN cc_start: 0.7819 (m110) cc_final: 0.7574 (m110)
REVERT: L  167 ASP cc_start: 0.8939 (t0) cc_final: 0.8419 (t0)
REVERT: L  170 ASP cc_start: 0.8699 (p0) cc_final: 0.8486 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 76
  average time/residue: 1.5468
  time to fit residues: 121.4557
Evaluate side-chains
  63 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
H 109 GLN
L 137 ASN
L 152 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.059933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.049185 restraints weight = 12833.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 2.86
r_work: 0.2622 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   4909  Z= 0.470
  Angle     :  0.631   7.028   6682  Z= 0.330
  Chirality :  0.045   0.142    737
  Planarity :  0.005   0.068    858
  Dihedral  :  5.282  35.421    699
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.36 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.34), residues: 613
  helix: -4.53 (0.66), residues: 26
  sheet:  0.50 (0.33), residues: 246
  loop : -0.25 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.005   0.002   HIS H  72 
 PHE   0.011   0.001   PHE L  71 
 TYR   0.018   0.002   TYR A 495 
 ARG   0.012   0.001   ARG L  24 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9166 (m-30) cc_final: 0.8660 (m-30)
REVERT: A  462 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8681 (mtmm)
REVERT: A  516 GLU cc_start: 0.8043 (pp20) cc_final: 0.7479 (pp20)
REVERT: H    3 GLN cc_start: 0.8232 (mm110) cc_final: 0.7958 (mp10)
REVERT: H   88 GLU cc_start: 0.9081 (pm20) cc_final: 0.8703 (pm20)
REVERT: H  205 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8620 (tptp)
REVERT: L  158 ASN cc_start: 0.7914 (m110) cc_final: 0.7687 (m110)
REVERT: L  167 ASP cc_start: 0.8918 (t0) cc_final: 0.8404 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 66
  average time/residue: 1.2661
  time to fit residues: 87.0639
Evaluate side-chains
  66 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   chunk 20 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.062754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.052040 restraints weight = 12617.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.93
r_work: 0.2711 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4909  Z= 0.204
  Angle     :  0.511   6.697   6682  Z= 0.268
  Chirality :  0.043   0.148    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.592  23.151    699
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.43 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.34), residues: 613
  helix: -4.51 (0.60), residues: 26
  sheet:  0.68 (0.33), residues: 244
  loop : -0.21 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 158 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.006   0.001   PHE L  71 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.007   0.001   ARG L  24 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9187 (m-30) cc_final: 0.8664 (m-30)
REVERT: A  462 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8691 (mtmm)
REVERT: A  516 GLU cc_start: 0.8197 (pp20) cc_final: 0.7575 (pp20)
REVERT: A  528 LYS cc_start: 0.6469 (tttt) cc_final: 0.4920 (pptt)
REVERT: H    3 GLN cc_start: 0.8394 (mm110) cc_final: 0.8108 (mp10)
REVERT: H   88 GLU cc_start: 0.9096 (pm20) cc_final: 0.8769 (pm20)
REVERT: H  205 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8935 (mmmt)
REVERT: L   17 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8133 (mt-10)
REVERT: L   81 GLU cc_start: 0.9242 (pm20) cc_final: 0.9022 (pm20)
REVERT: L  142 ARG cc_start: 0.9127 (tpp80) cc_final: 0.8408 (ttp80)
REVERT: L  167 ASP cc_start: 0.9029 (t0) cc_final: 0.8515 (t0)
REVERT: L  170 ASP cc_start: 0.8735 (p0) cc_final: 0.8483 (p0)
  outliers start: 9
  outliers final: 3
  residues processed: 72
  average time/residue: 1.3621
  time to fit residues: 101.8705
Evaluate side-chains
  65 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue  145 LEU
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   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 414 GLN
L 155 GLN
L 158 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.063056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.052301 restraints weight = 12637.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 2.94
r_work: 0.2717 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4909  Z= 0.216
  Angle     :  0.508   6.655   6682  Z= 0.264
  Chirality :  0.043   0.143    737
  Planarity :  0.004   0.063    858
  Dihedral  :  4.425  20.146    699
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.31 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.35), residues: 613
  helix: -4.45 (0.60), residues: 26
  sheet:  0.83 (0.33), residues: 243
  loop : -0.13 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.006   0.001   PHE L  98 
 TYR   0.012   0.001   TYR L 186 
 ARG   0.007   0.001   ARG H  19 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9183 (m-30) cc_final: 0.8632 (m-30)
REVERT: A  462 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8692 (mtmm)
REVERT: A  516 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7739 (pp20)
REVERT: A  528 LYS cc_start: 0.6458 (tttt) cc_final: 0.4924 (pptt)
REVERT: H    3 GLN cc_start: 0.8393 (mm110) cc_final: 0.8103 (mp10)
REVERT: H   88 GLU cc_start: 0.9132 (pm20) cc_final: 0.8901 (pm20)
REVERT: H  205 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8915 (mmmt)
REVERT: L   13 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9072 (mm)
REVERT: L   17 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8097 (mt-10)
REVERT: L   81 GLU cc_start: 0.9173 (pm20) cc_final: 0.8924 (pm20)
REVERT: L  167 ASP cc_start: 0.8988 (t0) cc_final: 0.8236 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 73
  average time/residue: 1.4211
  time to fit residues: 107.4936
Evaluate side-chains
  68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue  145 LEU
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0010
   overall best weight:    0.6388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.063274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.052502 restraints weight = 12642.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.94
r_work: 0.2720 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4909  Z= 0.199
  Angle     :  0.493   6.609   6682  Z= 0.258
  Chirality :  0.042   0.144    737
  Planarity :  0.004   0.062    858
  Dihedral  :  4.247  20.027    699
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.82 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.35), residues: 613
  helix: -4.37 (0.62), residues: 26
  sheet:  0.91 (0.33), residues: 243
  loop : -0.09 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.006   0.001   PHE L  98 
 TYR   0.014   0.001   TYR H  79 
 ARG   0.007   0.001   ARG H  19 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9187 (m-30) cc_final: 0.8628 (m-30)
REVERT: A  462 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8676 (mtmm)
REVERT: A  516 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7527 (pp20)
REVERT: A  518 LEU cc_start: 0.9009 (mt) cc_final: 0.8747 (mp)
REVERT: A  528 LYS cc_start: 0.6487 (tttt) cc_final: 0.4938 (pptt)
REVERT: H    3 GLN cc_start: 0.8394 (mm110) cc_final: 0.8097 (mp10)
REVERT: H   88 GLU cc_start: 0.9108 (pm20) cc_final: 0.8799 (pm20)
REVERT: H  205 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8896 (mmmt)
REVERT: L   13 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9042 (mm)
REVERT: L  142 ARG cc_start: 0.9128 (tpp80) cc_final: 0.8361 (ttp80)
REVERT: L  167 ASP cc_start: 0.8953 (t0) cc_final: 0.8508 (t0)
REVERT: L  170 ASP cc_start: 0.8696 (p0) cc_final: 0.8438 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 67
  average time/residue: 1.2879
  time to fit residues: 90.0002
Evaluate side-chains
  72 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue  145 LEU
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.6438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.063252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.052517 restraints weight = 12442.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.91
r_work: 0.2723 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4909  Z= 0.199
  Angle     :  0.490   6.602   6682  Z= 0.257
  Chirality :  0.042   0.140    737
  Planarity :  0.004   0.062    858
  Dihedral  :  4.189  20.236    699
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.01 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.35), residues: 613
  helix: -4.35 (0.61), residues: 26
  sheet:  0.94 (0.33), residues: 244
  loop : -0.10 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS H  72 
 PHE   0.005   0.001   PHE L  98 
 TYR   0.013   0.001   TYR L 192 
 ARG   0.009   0.001   ARG H  19 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9176 (m-30) cc_final: 0.8591 (m-30)
REVERT: A  430 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8979 (p)
REVERT: A  462 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8669 (mtmm)
REVERT: A  516 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7556 (pp20)
REVERT: A  528 LYS cc_start: 0.6469 (tttt) cc_final: 0.4919 (pptt)
REVERT: H    3 GLN cc_start: 0.8392 (mm110) cc_final: 0.8069 (mp10)
REVERT: H   88 GLU cc_start: 0.9107 (pm20) cc_final: 0.8784 (pm20)
REVERT: H  205 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8882 (mmmt)
REVERT: L   13 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9085 (mm)
REVERT: L   17 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: L   81 GLU cc_start: 0.9140 (pm20) cc_final: 0.8929 (pm20)
REVERT: L  142 ARG cc_start: 0.9123 (tpp80) cc_final: 0.8755 (ttt-90)
REVERT: L  167 ASP cc_start: 0.8984 (t0) cc_final: 0.8267 (t0)
REVERT: L  170 ASP cc_start: 0.8658 (p0) cc_final: 0.8429 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 1.2865
  time to fit residues: 96.3897
Evaluate side-chains
  71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue  145 LEU
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 0 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.063053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.052095 restraints weight = 12591.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.97
r_work: 0.2712 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4909  Z= 0.238
  Angle     :  0.534   8.386   6682  Z= 0.273
  Chirality :  0.043   0.134    737
  Planarity :  0.004   0.062    858
  Dihedral  :  4.275  20.514    699
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.63 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.35), residues: 613
  helix: -4.34 (0.62), residues: 26
  sheet:  0.91 (0.33), residues: 243
  loop : -0.05 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.006   0.001   PHE L  71 
 TYR   0.016   0.001   TYR H  79 
 ARG   0.009   0.001   ARG H  19 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.8983 (p)
REVERT: A  462 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8659 (mtmm)
REVERT: A  528 LYS cc_start: 0.6511 (tttt) cc_final: 0.4939 (pptt)
REVERT: H    3 GLN cc_start: 0.8378 (mm110) cc_final: 0.8047 (mp10)
REVERT: H   88 GLU cc_start: 0.9125 (pm20) cc_final: 0.8800 (pm20)
REVERT: H  205 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8877 (mmmt)
REVERT: L   13 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9082 (mm)
REVERT: L  142 ARG cc_start: 0.9136 (tpp80) cc_final: 0.8359 (ttp80)
REVERT: L  147 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.6015 (mt0)
REVERT: L  165 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8691 (pm20)
REVERT: L  167 ASP cc_start: 0.8901 (t0) cc_final: 0.8256 (t0)
REVERT: L  170 ASP cc_start: 0.8637 (p0) cc_final: 0.8421 (p0)
  outliers start: 13
  outliers final: 6
  residues processed: 69
  average time/residue: 1.3053
  time to fit residues: 93.9064
Evaluate side-chains
  70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue  145 LEU
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.0970
   chunk 42 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 37 optimal weight:    0.1980
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.5178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.063917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.052986 restraints weight = 12476.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 2.96
r_work: 0.2731 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4909  Z= 0.181
  Angle     :  0.505   6.574   6682  Z= 0.263
  Chirality :  0.042   0.137    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.118  19.841    699
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.57 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.35), residues: 613
  helix: -4.30 (0.60), residues: 26
  sheet:  0.96 (0.34), residues: 244
  loop : -0.06 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS H  72 
 PHE   0.005   0.001   PHE L 209 
 TYR   0.016   0.001   TYR H  79 
 ARG   0.004   0.000   ARG H  86 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8959 (p)
REVERT: A  462 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8634 (mtmm)
REVERT: A  516 GLU cc_start: 0.8159 (pp20) cc_final: 0.7600 (pp20)
REVERT: A  528 LYS cc_start: 0.6486 (tttt) cc_final: 0.4949 (pptt)
REVERT: H    3 GLN cc_start: 0.8372 (mm110) cc_final: 0.8040 (mp10)
REVERT: H   86 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.8037 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9126 (pm20) cc_final: 0.8823 (pm20)
REVERT: H  205 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8865 (mmmt)
REVERT: L   13 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9051 (mm)
REVERT: L  142 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8351 (ttp80)
REVERT: L  147 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5978 (mt0)
REVERT: L  165 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8648 (pm20)
REVERT: L  167 ASP cc_start: 0.8884 (t0) cc_final: 0.8244 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 72
  average time/residue: 1.3877
  time to fit residues: 103.8101
Evaluate side-chains
  72 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.062699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.052047 restraints weight = 12483.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.90
r_work: 0.2710 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4909  Z= 0.258
  Angle     :  0.571   9.391   6682  Z= 0.291
  Chirality :  0.043   0.137    737
  Planarity :  0.004   0.063    858
  Dihedral  :  4.308  20.780    699
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.76 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.35), residues: 613
  helix: -4.34 (0.63), residues: 26
  sheet:  0.96 (0.33), residues: 242
  loop :  0.00 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.006   0.001   PHE L  71 
 TYR   0.014   0.001   TYR H  79 
 ARG   0.004   0.000   ARG H  86 

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8982 (p)
REVERT: A  462 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8618 (mtmm)
REVERT: A  516 GLU cc_start: 0.8146 (pp20) cc_final: 0.7645 (pp20)
REVERT: A  528 LYS cc_start: 0.6502 (tttt) cc_final: 0.4915 (pptt)
REVERT: H    3 GLN cc_start: 0.8377 (mm110) cc_final: 0.8037 (mp10)
REVERT: H   88 GLU cc_start: 0.9124 (pm20) cc_final: 0.8778 (pm20)
REVERT: H  205 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8879 (mmmt)
REVERT: L   13 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9082 (mm)
REVERT: L  142 ARG cc_start: 0.9130 (tpp80) cc_final: 0.8353 (ttp80)
REVERT: L  147 GLN cc_start: 0.6481 (OUTLIER) cc_final: 0.6070 (mt0)
REVERT: L  165 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8666 (pm20)
REVERT: L  167 ASP cc_start: 0.8920 (t0) cc_final: 0.8291 (t0)
REVERT: L  170 ASP cc_start: 0.8699 (p0) cc_final: 0.8423 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 1.2893
  time to fit residues: 92.7731
Evaluate side-chains
  73 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.062808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.052132 restraints weight = 12659.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.92
r_work: 0.2714 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4909  Z= 0.240
  Angle     :  0.559   8.151   6682  Z= 0.290
  Chirality :  0.043   0.146    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.297  20.414    699
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.95 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.35), residues: 613
  helix: -4.36 (0.61), residues: 26
  sheet:  0.95 (0.33), residues: 242
  loop : -0.00 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.005   0.001   PHE L  71 
 TYR   0.018   0.001   TYR H  79 
 ARG   0.004   0.000   ARG H  86 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3559.22 seconds
wall clock time: 64 minutes 28.76 seconds (3868.76 seconds total)