Starting phenix.real_space_refine
on Wed Mar  5 23:22:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r4c_18885/03_2025/8r4c_18885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r4c_18885/03_2025/8r4c_18885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r4c_18885/03_2025/8r4c_18885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r4c_18885/03_2025/8r4c_18885.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r4c_18885/03_2025/8r4c_18885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r4c_18885/03_2025/8r4c_18885.cif"
  }
  resolution = 3.55
  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=   0.140
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       9      5.16       5
     C    2541      2.51       5
     N     669      2.21       5
     O     808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4027
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 843
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 3184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3184
          Classifications: {'peptide': 437}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 22, 'TRANS': 414}
          Unresolved non-hydrogen bonds: 172
          Unresolved non-hydrogen angles: 205
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 95
  Time building chain proxies: 2.88, per 1000 atoms: 0.72
  Number of scatterers: 4027
  At special positions: 0
  Unit cell: (54.6476, 73.3429, 104.981, 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       9     16.00
     O     808      8.00
     N     669      7.00
     C    2541      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " 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
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 514.1 milliseconds
  

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1054

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 6 sheets defined
      19.7% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.848A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4 through 15
    Processing helix  chain 'A' and resid 51 through 62
      removed outlier: 3.736A  pdb=" N   ILE A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN A  57 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
      Proline residue:  A  58  - end of helix
      removed outlier: 3.617A  pdb=" N   LEU A  62 " --> pdb=" O   PRO A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 4.089A  pdb=" N   SER A 127 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 150
      removed outlier: 3.522A  pdb=" N   SER A 149 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 172
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 4.089A  pdb=" N   GLU A 214 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.904A  pdb=" N   SER A 237 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 260
    Processing helix  chain 'A' and resid 298 through 302
    Processing helix  chain 'A' and resid 320 through 324
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.740A  pdb=" N   LEU A 345 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 392
    Processing helix  chain 'A' and resid 419 through 426
      removed outlier: 3.790A  pdb=" N   GLY A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 439
    Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.184A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   VAL C  33 " --> pdb=" O   ASP C  98 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   MET C  34 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   SER C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.184A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   GLY C  99 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   ASN C 107 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ILE C 101 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   TYR C 105 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 19 through 20
      removed outlier: 6.297A  pdb=" N   GLU A  19 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY A  30 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA A  41 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU A 222 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267
      removed outlier: 6.842A  pdb=" N   LEU A 310 " --> pdb=" O   TRP A 333 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 377
      removed outlier: 6.411A  pdb=" N   GLU A 396 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)

    111 hydrogen bonds defined for protein.
    240 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: 1.15

  Time building geometry restraints manager: 1.18 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: 1323
        1.34 -     1.46: 526
        1.46 -     1.57: 2222
        1.57 -     1.69: 0
        1.69 -     1.81: 15
  Bond restraints: 4086
  Sorted by residual:
  bond pdb=" N   PRO A 414 "
       pdb=" CA  PRO A 414 "
    ideal  model  delta    sigma   weight residual
    1.469  1.485 -0.016 1.28e-02 6.10e+03 1.57e+00
  bond pdb=" CB  ILE A 144 "
       pdb=" CG1 ILE A 144 "
    ideal  model  delta    sigma   weight residual
    1.530  1.554 -0.024 2.00e-02 2.50e+03 1.42e+00
  bond pdb=" CA  ILE A 144 "
       pdb=" CB  ILE A 144 "
    ideal  model  delta    sigma   weight residual
    1.540  1.556 -0.016 1.36e-02 5.41e+03 1.40e+00
  bond pdb=" CB  VAL C  48 "
       pdb=" CG2 VAL C  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.92e-01
  bond pdb=" CB  CYS C  95 "
       pdb=" SG  CYS C  95 "
    ideal  model  delta    sigma   weight residual
    1.808  1.780  0.028 3.30e-02 9.18e+02 7.39e-01
  ... (remaining 4081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 5359
        1.54 -     3.08: 174
        3.08 -     4.63: 38
        4.63 -     6.17: 11
        6.17 -     7.71: 5
  Bond angle restraints: 5587
  Sorted by residual:
  angle pdb=" N   ILE A 166 "
        pdb=" CA  ILE A 166 "
        pdb=" C   ILE A 166 "
      ideal   model   delta    sigma   weight residual
     113.20  109.27    3.93 9.60e-01 1.09e+00 1.68e+01
  angle pdb=" CB  ILE A 144 "
        pdb=" CG1 ILE A 144 "
        pdb=" CD1 ILE A 144 "
      ideal   model   delta    sigma   weight residual
     113.80  121.51   -7.71 2.10e+00 2.27e-01 1.35e+01
  angle pdb=" CA  ILE A 144 "
        pdb=" CB  ILE A 144 "
        pdb=" CG1 ILE A 144 "
      ideal   model   delta    sigma   weight residual
     110.40  116.38   -5.98 1.70e+00 3.46e-01 1.24e+01
  angle pdb=" CA  GLN A  12 "
        pdb=" CB  GLN A  12 "
        pdb=" CG  GLN A  12 "
      ideal   model   delta    sigma   weight residual
     114.10  120.42   -6.32 2.00e+00 2.50e-01 9.99e+00
  angle pdb=" N   ALA C  91 "
        pdb=" CA  ALA C  91 "
        pdb=" C   ALA C  91 "
      ideal   model   delta    sigma   weight residual
     108.34  112.10   -3.76 1.31e+00 5.83e-01 8.24e+00
  ... (remaining 5582 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 2071
       16.71 -    33.43: 319
       33.43 -    50.14: 88
       50.14 -    66.85: 16
       66.85 -    83.56: 7
  Dihedral angle restraints: 2501
    sinusoidal: 886
      harmonic: 1615
  Sorted by residual:
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  95 "
           pdb=" CB  CYS C  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.85  -74.85     1      1.00e+01 1.00e-02 7.09e+01
  dihedral pdb=" CA  LYS A 173 "
           pdb=" C   LYS A 173 "
           pdb=" N   SER A 174 "
           pdb=" CA  SER A 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.72   19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  SER A 203 "
           pdb=" C   SER A 203 "
           pdb=" N   SER A 204 "
           pdb=" CA  SER A 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.90  -18.10     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 2498 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 417
       0.033 -    0.066: 196
       0.066 -    0.099: 61
       0.099 -    0.131: 25
       0.131 -    0.164: 2
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" CA  ILE A 408 "
            pdb=" N   ILE A 408 "
            pdb=" C   ILE A 408 "
            pdb=" CB  ILE A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CB  ILE A 144 "
            pdb=" CA  ILE A 144 "
            pdb=" CG1 ILE A 144 "
            pdb=" CG2 ILE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE A 210 "
            pdb=" N   ILE A 210 "
            pdb=" C   ILE A 210 "
            pdb=" CB  ILE A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 698 not shown)

  Planarity restraints: 715
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 413 "    0.031 5.00e-02 4.00e+02   4.68e-02 3.51e+00
        pdb=" N   PRO A 414 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 414 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 414 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 189 "   -0.030 5.00e-02 4.00e+02   4.53e-02 3.28e+00
        pdb=" N   PRO A 190 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 190 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 190 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 233 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A 234 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 712 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 404
        2.75 -     3.28: 3926
        3.28 -     3.82: 6653
        3.82 -     4.36: 8050
        4.36 -     4.90: 13681
  Nonbonded interactions: 32714
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C  32 "
            pdb=" OH  TYR A  45 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   SER A 417 "
            pdb=" OH  TYR A 433 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG1 THR A 154 "
            pdb=" OE1 GLU A 155 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   SER A 352 "
            pdb=" OG1 THR A 374 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   SER A 286 "
            pdb=" OG1 THR A 308 "
     model   vdw
     2.301 3.040
  ... (remaining 32709 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:             0.310
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.260
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4086  Z= 0.231
  Angle     :  0.718   7.710   5587  Z= 0.378
  Chirality :  0.044   0.164    701
  Planarity :  0.005   0.047    715
  Dihedral  : 17.999  83.565   1444
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 36.28 %
    Favored  : 62.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.95 (0.34), residues: 549
  helix: -1.38 (0.57), residues: 95
  sheet: -1.81 (0.43), residues: 135
  loop : -2.26 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  36 
 HIS   0.001   0.000   HIS C 109 
 PHE   0.014   0.002   PHE A 410 
 TYR   0.011   0.001   TYR C  37 
 ARG   0.007   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  214 GLU cc_start: 0.6355 (mp0) cc_final: 0.6038 (mp0)
REVERT: A  376 PHE cc_start: 0.8570 (t80) cc_final: 0.8106 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 129
  average time/residue: 0.1647
  time to fit residues: 26.1280
Evaluate side-chains
  129 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 126
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3352 r_free = 0.3352 target = 0.132885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.110713 restraints weight = 5577.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.113598 restraints weight = 3252.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.115493 restraints weight = 2295.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.0684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4086  Z= 0.252
  Angle     :  0.670   7.108   5587  Z= 0.341
  Chirality :  0.043   0.182    701
  Planarity :  0.005   0.044    715
  Dihedral  :  5.620  38.600    583
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 30.70 %
    Favored  : 62.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.91 (0.34), residues: 549
  helix: -1.26 (0.56), residues: 102
  sheet: -1.86 (0.44), residues: 130
  loop : -2.24 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.015   0.002   PHE A 410 
 TYR   0.008   0.001   TYR C  94 
 ARG   0.005   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.431 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7151 (tp40) cc_final: 0.6525 (tp40)
REVERT: C   45 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7374 (mtt180)
REVERT: A  214 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5898 (mp0)
REVERT: A  257 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5600 (tt)
REVERT: A  301 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7109 (tt)
  outliers start: 29
  outliers final: 19
  residues processed: 138
  average time/residue: 0.1613
  time to fit residues: 27.4645
Evaluate side-chains
  143 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3371 r_free = 0.3371 target = 0.134733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.112615 restraints weight = 5524.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.115509 restraints weight = 3203.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.117551 restraints weight = 2252.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.0852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4086  Z= 0.226
  Angle     :  0.656   8.609   5587  Z= 0.330
  Chirality :  0.043   0.179    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.380  49.345    576
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  8.84 %
    Allowed  : 29.07 %
    Favored  : 62.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.85 (0.34), residues: 549
  helix: -1.22 (0.57), residues: 102
  sheet: -1.87 (0.44), residues: 130
  loop : -2.17 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  36 
 HIS   0.001   0.000   HIS C 109 
 PHE   0.014   0.002   PHE A 410 
 TYR   0.007   0.001   TYR C  94 
 ARG   0.006   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 0.426 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7238 (tp40) cc_final: 0.6932 (tp40)
REVERT: C   45 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7346 (mtt180)
REVERT: A   29 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7599 (mttt)
REVERT: A   54 ARG cc_start: 0.7606 (mtm110) cc_final: 0.6940 (ttp80)
REVERT: A  155 GLU cc_start: 0.8281 (mp0) cc_final: 0.7883 (mp0)
REVERT: A  214 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5737 (mp0)
REVERT: A  257 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5522 (tt)
REVERT: A  301 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7107 (tt)
REVERT: A  338 GLN cc_start: 0.7836 (mp10) cc_final: 0.7402 (mp10)
REVERT: A  432 GLN cc_start: 0.7549 (mt0) cc_final: 0.7291 (mt0)
  outliers start: 38
  outliers final: 26
  residues processed: 139
  average time/residue: 0.1616
  time to fit residues: 27.6172
Evaluate side-chains
  149 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0470
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.2086

-------------------------------------------------------------------------------
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 = 0.3322 r_free = 0.3322 target = 0.130585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.108237 restraints weight = 5614.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.111057 restraints weight = 3300.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.112763 restraints weight = 2351.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   4086  Z= 0.372
  Angle     :  0.738   7.339   5587  Z= 0.372
  Chirality :  0.046   0.177    701
  Planarity :  0.005   0.045    715
  Dihedral  :  5.842  58.303    576
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  9.77 %
    Allowed  : 30.23 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.81 (0.35), residues: 549
  helix: -1.11 (0.60), residues: 95
  sheet: -1.89 (0.45), residues: 130
  loop : -2.14 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  36 
 HIS   0.002   0.001   HIS C 109 
 PHE   0.014   0.002   PHE A 115 
 TYR   0.009   0.002   TYR C  94 
 ARG   0.007   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 125
  time to evaluate  : 0.427 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7233 (tp40) cc_final: 0.6914 (tp40)
REVERT: C   45 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7077 (mtt180)
REVERT: A  257 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5680 (tt)
REVERT: A  301 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6953 (tt)
REVERT: A  338 GLN cc_start: 0.7810 (mp10) cc_final: 0.7342 (mp10)
  outliers start: 42
  outliers final: 32
  residues processed: 146
  average time/residue: 0.1507
  time to fit residues: 27.3724
Evaluate side-chains
  154 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 10 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 15 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.133897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.111223 restraints weight = 5807.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.114126 restraints weight = 3325.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.116095 restraints weight = 2327.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4086  Z= 0.200
  Angle     :  0.644   6.988   5587  Z= 0.324
  Chirality :  0.043   0.170    701
  Planarity :  0.005   0.041    715
  Dihedral  :  5.416  52.099    576
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 32.33 %
    Favored  : 60.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.83 (0.34), residues: 549
  helix: -1.16 (0.57), residues: 102
  sheet: -1.89 (0.45), residues: 130
  loop : -2.16 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  36 
 HIS   0.001   0.000   HIS C 109 
 PHE   0.016   0.002   PHE A 410 
 TYR   0.005   0.001   TYR C  37 
 ARG   0.005   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.396 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7307 (tp40) cc_final: 0.6845 (tp40)
REVERT: C   45 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7221 (mtt180)
REVERT: C  117 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8355 (m)
REVERT: A   54 ARG cc_start: 0.7467 (mtm110) cc_final: 0.6867 (ttp80)
REVERT: A  155 GLU cc_start: 0.8288 (mp0) cc_final: 0.7892 (mp0)
REVERT: A  257 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5732 (tt)
REVERT: A  301 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7141 (tt)
REVERT: A  338 GLN cc_start: 0.7753 (mp-120) cc_final: 0.7354 (mp10)
  outliers start: 32
  outliers final: 26
  residues processed: 142
  average time/residue: 0.1577
  time to fit residues: 27.8664
Evaluate side-chains
  154 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.133460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.111111 restraints weight = 5546.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.113966 restraints weight = 3221.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.115793 restraints weight = 2279.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4086  Z= 0.243
  Angle     :  0.668   7.057   5587  Z= 0.333
  Chirality :  0.044   0.175    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.326  44.809    576
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  9.53 %
    Allowed  : 30.00 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.77 (0.35), residues: 549
  helix: -1.07 (0.60), residues: 95
  sheet: -1.96 (0.44), residues: 130
  loop : -2.06 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.014   0.002   PHE A 115 
 TYR   0.006   0.001   TYR C  37 
 ARG   0.007   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 124
  time to evaluate  : 0.425 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7293 (tp40) cc_final: 0.6793 (tp40)
REVERT: C   45 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7247 (mtt180)
REVERT: A  155 GLU cc_start: 0.8313 (mp0) cc_final: 0.7868 (mp0)
REVERT: A  257 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5383 (tt)
REVERT: A  301 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7042 (tt)
REVERT: A  338 GLN cc_start: 0.7950 (mp-120) cc_final: 0.7491 (mp10)
  outliers start: 41
  outliers final: 34
  residues processed: 148
  average time/residue: 0.1543
  time to fit residues: 28.3042
Evaluate side-chains
  160 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  423 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.0030
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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 = 0.3349 r_free = 0.3349 target = 0.133362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.111083 restraints weight = 5659.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.114004 restraints weight = 3260.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.115876 restraints weight = 2282.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4086  Z= 0.230
  Angle     :  0.669   8.024   5587  Z= 0.335
  Chirality :  0.043   0.173    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.158  36.206    576
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  9.30 %
    Allowed  : 30.47 %
    Favored  : 60.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.85 (0.35), residues: 549
  helix: -1.18 (0.58), residues: 103
  sheet: -1.94 (0.44), residues: 131
  loop : -2.16 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.014   0.002   PHE A 115 
 TYR   0.006   0.001   TYR C  37 
 ARG   0.008   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.463 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7289 (tp40) cc_final: 0.6770 (tp40)
REVERT: C   45 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7212 (mtt180)
REVERT: A   54 ARG cc_start: 0.7438 (mtm110) cc_final: 0.6903 (ttp80)
REVERT: A  257 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5470 (tt)
REVERT: A  301 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7050 (tt)
REVERT: A  338 GLN cc_start: 0.7930 (mp-120) cc_final: 0.7478 (mp10)
  outliers start: 40
  outliers final: 34
  residues processed: 149
  average time/residue: 0.1556
  time to fit residues: 28.7002
Evaluate side-chains
  162 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 126
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3350 r_free = 0.3350 target = 0.133421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.111271 restraints weight = 5479.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.114102 restraints weight = 3194.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.115790 restraints weight = 2269.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4086  Z= 0.279
  Angle     :  0.705   7.204   5587  Z= 0.352
  Chirality :  0.045   0.176    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.274  35.503    576
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  9.77 %
    Allowed  : 29.77 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.83 (0.35), residues: 549
  helix: -1.15 (0.60), residues: 96
  sheet: -2.02 (0.44), residues: 130
  loop : -2.09 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.013   0.002   PHE A 115 
 TYR   0.007   0.001   TYR C  94 
 ARG   0.008   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 128
  time to evaluate  : 0.417 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7313 (tp40) cc_final: 0.6786 (tp40)
REVERT: C   45 ARG cc_start: 0.7686 (mtm180) cc_final: 0.7226 (mtt180)
REVERT: A   54 ARG cc_start: 0.6866 (mtm110) cc_final: 0.6364 (ttp80)
REVERT: A  155 GLU cc_start: 0.8275 (mp0) cc_final: 0.7913 (mp0)
REVERT: A  257 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5492 (tt)
REVERT: A  301 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7033 (tt)
REVERT: A  338 GLN cc_start: 0.7942 (mp-120) cc_final: 0.7586 (mp10)
  outliers start: 42
  outliers final: 38
  residues processed: 153
  average time/residue: 0.1562
  time to fit residues: 29.5382
Evaluate side-chains
  166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  423 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.133058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.110756 restraints weight = 5602.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.113459 restraints weight = 3248.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.115474 restraints weight = 2315.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4086  Z= 0.283
  Angle     :  0.704   7.427   5587  Z= 0.352
  Chirality :  0.044   0.176    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.309  35.133    576
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 29.07 %
    Favored  : 60.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.97 (0.34), residues: 549
  helix: -1.31 (0.57), residues: 103
  sheet: -2.00 (0.45), residues: 130
  loop : -2.23 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.018   0.002   PHE A 434 
 TYR   0.006   0.001   TYR C  94 
 ARG   0.009   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 127
  time to evaluate  : 0.466 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7325 (tp40) cc_final: 0.6088 (tp40)
REVERT: C   45 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7146 (mtt180)
REVERT: A   54 ARG cc_start: 0.7170 (mtm110) cc_final: 0.6582 (ttp80)
REVERT: A  155 GLU cc_start: 0.8270 (mp0) cc_final: 0.7915 (mp0)
REVERT: A  214 GLU cc_start: 0.5928 (mp0) cc_final: 0.5522 (mp0)
REVERT: A  257 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5782 (tt)
REVERT: A  301 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7034 (tt)
REVERT: A  338 GLN cc_start: 0.7934 (mp-120) cc_final: 0.7588 (mp10)
  outliers start: 43
  outliers final: 38
  residues processed: 153
  average time/residue: 0.1442
  time to fit residues: 27.4976
Evaluate side-chains
  166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  423 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.132259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.110028 restraints weight = 5587.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.112675 restraints weight = 3264.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.114680 restraints weight = 2327.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4086  Z= 0.267
  Angle     :  0.699   7.328   5587  Z= 0.350
  Chirality :  0.044   0.174    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.285  34.125    576
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  9.07 %
    Allowed  : 30.47 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.85 (0.34), residues: 549
  helix: -1.21 (0.60), residues: 96
  sheet: -1.97 (0.44), residues: 131
  loop : -2.11 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.017   0.002   PHE A 434 
 TYR   0.007   0.001   TYR C  94 
 ARG   0.008   0.001   ARG A 270 

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 128
  time to evaluate  : 0.415 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7325 (tp40) cc_final: 0.6093 (tp40)
REVERT: C   45 ARG cc_start: 0.7723 (mtm180) cc_final: 0.7182 (mtt180)
REVERT: A   54 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6564 (ttp80)
REVERT: A  155 GLU cc_start: 0.8281 (mp0) cc_final: 0.7903 (mp0)
REVERT: A  257 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5434 (tt)
REVERT: A  301 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7029 (tt)
REVERT: A  338 GLN cc_start: 0.7934 (mp-120) cc_final: 0.7476 (mp10)
  outliers start: 39
  outliers final: 37
  residues processed: 150
  average time/residue: 0.1538
  time to fit residues: 28.6716
Evaluate side-chains
  168 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  423 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0030
   chunk 11 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0370
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0970
   chunk 10 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.2666

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.138544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.116440 restraints weight = 5476.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.119342 restraints weight = 3122.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.121390 restraints weight = 2186.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4086  Z= 0.175
  Angle     :  0.638   7.067   5587  Z= 0.318
  Chirality :  0.043   0.168    701
  Planarity :  0.005   0.041    715
  Dihedral  :  4.858  25.526    576
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 32.79 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.86 (0.35), residues: 549
  helix: -1.39 (0.55), residues: 109
  sheet: -1.90 (0.45), residues: 131
  loop : -2.11 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  36 
 HIS   0.001   0.000   HIS C 109 
 PHE   0.015   0.002   PHE A 115 
 TYR   0.005   0.001   TYR C  37 
 ARG   0.007   0.001   ARG A 270 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1698.49 seconds
wall clock time: 30 minutes 7.89 seconds (1807.89 seconds total)