Starting phenix.real_space_refine
on Mon Jan 13 20:55:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r4c_18885/01_2025/8r4c_18885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r4c_18885/01_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_18885/01_2025/8r4c_18885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r4c_18885/01_2025/8r4c_18885.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r4c_18885/01_2025/8r4c_18885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r4c_18885/01_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-5571/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: 2.91, 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: 1.02
  Conformation dependent library (CDL) restraints added in 548.3 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: 0.51
  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: 1.14

  Time building geometry restraints manager: 1.16 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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.970
  Find NCS groups from input model:        0.040
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.310
-------------------------------------------------------------------------------
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  : 0.428 
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: 0.1678
  time to fit residues: 26.5925
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  : 0.478 
-------------------------------------------------------------------------------
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 = 0.132886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.110725 restraints weight = 5577.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.113618 restraints weight = 3246.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.115441 restraints weight = 2292.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
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  : 0.436 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7145 (tp40) cc_final: 0.6513 (tp40)
REVERT: C   45 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7364 (mtt180)
REVERT: A  214 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5892 (mp0)
REVERT: A  257 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5593 (tt)
REVERT: A  301 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7105 (tt)
  outliers start: 29
  outliers final: 19
  residues processed: 138
  average time/residue: 0.1653
  time to fit residues: 28.0557
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  : 0.453 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0270
   chunk 45 optimal weight:    0.3980
   chunk 43 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.2836

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.138504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.116293 restraints weight = 5499.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.119250 restraints weight = 3170.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.121145 restraints weight = 2233.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4086  Z= 0.176
  Angle     :  0.625   9.172   5587  Z= 0.314
  Chirality :  0.042   0.177    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.156  46.910    576
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  8.14 %
    Allowed  : 29.07 %
    Favored  : 62.79 %
  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: -2.74 (0.34), residues: 549
  helix: -1.19 (0.57), residues: 102
  sheet: -1.69 (0.45), residues: 132
  loop : -2.13 (0.32), residues: 315

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   0.015   0.002   PHE A 410 
 TYR   0.006   0.001   TYR C  94 
 ARG   0.006   0.001   ARG A  54 

*********************** 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
  165 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 0.460 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7232 (tp40) cc_final: 0.6921 (tp40)
REVERT: C   45 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7320 (mtt180)
REVERT: A   13 GLU cc_start: 0.7027 (tp30) cc_final: 0.6736 (tp30)
REVERT: A  155 GLU cc_start: 0.8277 (mp0) cc_final: 0.7861 (mp0)
REVERT: A  214 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5628 (mp0)
REVERT: A  257 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5469 (tt)
REVERT: A  301 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7295 (tt)
REVERT: A  338 GLN cc_start: 0.7850 (mp-120) cc_final: 0.7276 (mp10)
REVERT: A  432 GLN cc_start: 0.7605 (mt0) cc_final: 0.7339 (mt0)
  outliers start: 35
  outliers final: 22
  residues processed: 147
  average time/residue: 0.1569
  time to fit residues: 28.7725
Evaluate side-chains
  150 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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   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  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
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:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0980
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3329 r_free = 0.3329 target = 0.131332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.108880 restraints weight = 5612.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.111708 restraints weight = 3315.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.113563 restraints weight = 2372.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   4086  Z= 0.371
  Angle     :  0.723   7.356   5587  Z= 0.364
  Chirality :  0.045   0.180    701
  Planarity :  0.005   0.044    715
  Dihedral  :  5.733  57.266    576
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  9.77 %
    Allowed  : 29.30 %
    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: -2.76 (0.35), residues: 549
  helix: -1.09 (0.60), residues: 95
  sheet: -1.84 (0.45), residues: 130
  loop : -2.10 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.013   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
  163 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 121
  time to evaluate  : 0.434 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7245 (tp40) cc_final: 0.6929 (tp40)
REVERT: C   45 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7048 (mtt180)
REVERT: A   54 ARG cc_start: 0.7649 (mtm110) cc_final: 0.6856 (ttp80)
REVERT: A  151 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8445 (mmmt)
REVERT: A  257 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5619 (tt)
REVERT: A  301 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6980 (tt)
REVERT: A  338 GLN cc_start: 0.7962 (mp-120) cc_final: 0.7434 (mp10)
REVERT: A  432 GLN cc_start: 0.7730 (mt0) cc_final: 0.7513 (mt0)
  outliers start: 42
  outliers final: 30
  residues processed: 144
  average time/residue: 0.1637
  time to fit residues: 28.8721
Evaluate side-chains
  154 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 GLU
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 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  119 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
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  248 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  273 ILE
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  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:    0.8980
   chunk 10 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3347 r_free = 0.3347 target = 0.132740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.109542 restraints weight = 5797.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.112419 restraints weight = 3365.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.114420 restraints weight = 2379.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1040

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= 0.262
  Angle     :  0.671   7.101   5587  Z= 0.338
  Chirality :  0.043   0.177    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.610  56.935    576
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  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: -2.86 (0.34), residues: 549
  helix: -1.21 (0.58), residues: 102
  sheet: -1.86 (0.45), residues: 130
  loop : -2.19 (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 115 
 TYR   0.007   0.001   TYR C  94 
 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
  166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 123
  time to evaluate  : 0.431 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7209 (tp40) cc_final: 0.6877 (tp40)
REVERT: C   45 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.6955 (mtt180)
REVERT: A  151 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8401 (mmmt)
REVERT: A  155 GLU cc_start: 0.8313 (mp0) cc_final: 0.7923 (mp0)
REVERT: A  257 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5736 (tt)
REVERT: A  301 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7026 (tt)
REVERT: A  338 GLN cc_start: 0.7906 (mp-120) cc_final: 0.7419 (mp10)
  outliers start: 43
  outliers final: 31
  residues processed: 146
  average time/residue: 0.1622
  time to fit residues: 29.0397
Evaluate side-chains
  156 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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 A residue   18 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  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  185 ILE
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  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:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3331 r_free = 0.3331 target = 0.131450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.108722 restraints weight = 5654.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.111485 restraints weight = 3309.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.113416 restraints weight = 2353.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1146

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= 0.284
  Angle     :  0.689   7.158   5587  Z= 0.347
  Chirality :  0.044   0.174    701
  Planarity :  0.005   0.044    715
  Dihedral  :  5.559  51.629    576
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 28.37 %
    Favored  : 61.63 %
  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: -2.79 (0.34), residues: 549
  helix: -1.23 (0.59), residues: 96
  sheet: -1.86 (0.45), residues: 130
  loop : -2.08 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.014   0.002   PHE A 115 
 TYR   0.007   0.001   TYR C  94 
 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
  170 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 127
  time to evaluate  : 0.431 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7235 (tp40) cc_final: 0.6799 (tp40)
REVERT: C   45 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7255 (mtt180)
REVERT: A   54 ARG cc_start: 0.7468 (mtm110) cc_final: 0.6795 (ttp80)
REVERT: A  151 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8431 (mmmt)
REVERT: A  155 GLU cc_start: 0.8313 (mp0) cc_final: 0.7878 (mp0)
REVERT: A  257 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5375 (tt)
REVERT: A  301 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7011 (tt)
REVERT: A  338 GLN cc_start: 0.7932 (mp-120) cc_final: 0.7458 (mp10)
  outliers start: 43
  outliers final: 35
  residues processed: 149
  average time/residue: 0.1636
  time to fit residues: 29.9026
Evaluate side-chains
  166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
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   18 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   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  185 ILE
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  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  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:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.132752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.109851 restraints weight = 5710.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.112717 restraints weight = 3327.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.114660 restraints weight = 2355.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1159

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= 0.256
  Angle     :  0.665   7.226   5587  Z= 0.335
  Chirality :  0.043   0.165    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.395  45.556    576
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 28.60 %
    Favored  : 61.40 %
  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 (0.34), residues: 549
  helix: -1.27 (0.58), residues: 102
  sheet: -1.86 (0.45), residues: 130
  loop : -2.17 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   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 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
  170 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 127
  time to evaluate  : 0.457 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7338 (tp40) cc_final: 0.6861 (tp40)
REVERT: C   45 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7230 (mtt180)
REVERT: A   54 ARG cc_start: 0.6950 (mtm110) cc_final: 0.6429 (ttp80)
REVERT: A  257 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5480 (tt)
REVERT: A  301 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7010 (tt)
REVERT: A  338 GLN cc_start: 0.7934 (mp-120) cc_final: 0.7465 (mp10)
REVERT: A  395 MET cc_start: 0.6460 (mtt) cc_final: 0.6011 (mtt)
  outliers start: 43
  outliers final: 37
  residues processed: 152
  average time/residue: 0.1609
  time to fit residues: 30.1656
Evaluate side-chains
  166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 127
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
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   16 MET
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  153 LEU
Chi-restraints excluded: chain A residue  159 SER
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  248 SER
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  364 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3346 r_free = 0.3346 target = 0.132742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.110252 restraints weight = 5487.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.113077 restraints weight = 3224.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.114829 restraints weight = 2306.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4086  Z= 0.313
  Angle     :  0.705   7.411   5587  Z= 0.355
  Chirality :  0.045   0.173    701
  Planarity :  0.005   0.045    715
  Dihedral  :  5.497  42.430    576
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers : 10.47 %
    Allowed  : 29.07 %
    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: -2.80 (0.35), residues: 549
  helix: -1.24 (0.60), residues: 96
  sheet: -1.87 (0.45), residues: 130
  loop : -2.08 (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
  175 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 130
  time to evaluate  : 0.458 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7243 (tp40) cc_final: 0.6777 (tp40)
REVERT: C   45 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7246 (mtt180)
REVERT: A   54 ARG cc_start: 0.6879 (mtm110) cc_final: 0.6371 (ttp80)
REVERT: A  144 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7421 (pp)
REVERT: A  155 GLU cc_start: 0.8300 (mp0) cc_final: 0.7944 (mp0)
REVERT: A  257 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5602 (tt)
REVERT: A  301 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7032 (tt)
REVERT: A  338 GLN cc_start: 0.7786 (mp-120) cc_final: 0.7456 (mp10)
REVERT: A  395 MET cc_start: 0.6754 (mtt) cc_final: 0.6226 (mtt)
  outliers start: 45
  outliers final: 40
  residues processed: 156
  average time/residue: 0.1472
  time to fit residues: 29.0093
Evaluate side-chains
  173 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 130
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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   16 MET
Chi-restraints excluded: chain A residue   18 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  144 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 ILE
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  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  365 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
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:    0.0270
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7438

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.132803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.109952 restraints weight = 5674.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.112761 restraints weight = 3326.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.114604 restraints weight = 2357.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
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= 0.264
  Angle     :  0.677   7.246   5587  Z= 0.341
  Chirality :  0.043   0.171    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.344  37.559    576
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers : 10.70 %
    Allowed  : 28.14 %
    Favored  : 61.16 %
  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: -2.93 (0.34), residues: 549
  helix: -1.32 (0.57), residues: 103
  sheet: -1.91 (0.44), residues: 130
  loop : -2.22 (0.32), 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   0.014   0.002   PHE A 115 
 TYR   0.006   0.001   TYR C  94 
 ARG   0.008   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
  174 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 128
  time to evaluate  : 0.414 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7327 (tp40) cc_final: 0.6827 (tp40)
REVERT: C   45 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7204 (mtt180)
REVERT: A  144 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7397 (pp)
REVERT: A  155 GLU cc_start: 0.8296 (mp0) cc_final: 0.7917 (mp0)
REVERT: A  214 GLU cc_start: 0.5887 (mp0) cc_final: 0.5482 (mp0)
REVERT: A  257 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5733 (tt)
REVERT: A  301 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7016 (tt)
REVERT: A  338 GLN cc_start: 0.7930 (mp-120) cc_final: 0.7468 (mp10)
REVERT: A  395 MET cc_start: 0.6495 (mtt) cc_final: 0.6045 (mtt)
  outliers start: 46
  outliers final: 40
  residues processed: 155
  average time/residue: 0.1625
  time to fit residues: 31.1267
Evaluate side-chains
  168 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 125
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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   16 MET
Chi-restraints excluded: chain A residue   18 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  144 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 ILE
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  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 2 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   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 = 0.3343 r_free = 0.3343 target = 0.132312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.109825 restraints weight = 5624.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.112641 restraints weight = 3285.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.114625 restraints weight = 2320.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1323

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= 0.277
  Angle     :  0.691   7.498   5587  Z= 0.348
  Chirality :  0.044   0.171    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.351  35.305    576
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers : 10.47 %
    Allowed  : 27.67 %
    Favored  : 61.86 %
  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: -2.87 (0.34), residues: 549
  helix: -1.23 (0.60), residues: 96
  sheet: -1.98 (0.44), residues: 130
  loop : -2.12 (0.31), residues: 323

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
  171 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 126
  time to evaluate  : 0.490 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7323 (tp40) cc_final: 0.6054 (tp40)
REVERT: C   45 ARG cc_start: 0.7683 (mtm180) cc_final: 0.7104 (mtt180)
REVERT: A   54 ARG cc_start: 0.6918 (mtm110) cc_final: 0.6457 (ttp80)
REVERT: A  155 GLU cc_start: 0.8296 (mp0) cc_final: 0.7920 (mp0)
REVERT: A  257 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5466 (tt)
REVERT: A  301 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7002 (tt)
REVERT: A  338 GLN cc_start: 0.7846 (mp-120) cc_final: 0.7527 (mp10)
REVERT: A  395 MET cc_start: 0.6562 (mtt) cc_final: 0.6184 (mtt)
  outliers start: 45
  outliers final: 41
  residues processed: 152
  average time/residue: 0.1518
  time to fit residues: 29.0563
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  : 0.460 
-------------------------------------------------------------------------------
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    7 ILE
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   18 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  185 ILE
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  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:    0.0970
   chunk 11 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0970
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    0.2980
   overall best weight:    0.4376

-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.135231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.112830 restraints weight = 5570.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.115743 restraints weight = 3206.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.117700 restraints weight = 2243.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4086  Z= 0.205
  Angle     :  0.667   7.816   5587  Z= 0.337
  Chirality :  0.043   0.206    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.092  29.365    576
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  7.67 %
    Allowed  : 31.16 %
    Favored  : 61.16 %
  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: -2.92 (0.34), residues: 549
  helix: -1.44 (0.55), residues: 109
  sheet: -1.96 (0.44), residues: 131
  loop : -2.13 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 
 PHE   0.015   0.002   PHE A 115 
 TYR   0.007   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: 1613.84 seconds
wall clock time: 29 minutes 34.96 seconds (1774.96 seconds total)