Starting phenix.real_space_refine
on Fri May  9 20:03:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dep_27394/05_2025/8dep_27394.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dep_27394/05_2025/8dep_27394.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dep_27394/05_2025/8dep_27394.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dep_27394/05_2025/8dep_27394.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dep_27394/05_2025/8dep_27394.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dep_27394/05_2025/8dep_27394.cif"
  }
  resolution = 3.6
  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=   0.002 sd=   0.034
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       7      5.16       5
     C    2175      2.51       5
     N     489      2.21       5
     O     552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3223
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3062
          Classifications: {'peptide': 398}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 13, 'TRANS': 384}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 11, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 77
    Chain: "A"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 161
          Unusual residues: {'AJP': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 422
          Unresolved non-hydrogen chiralities: 81
  Time building chain proxies: 3.01, per 1000 atoms: 0.93
  Number of scatterers: 3223
  At special positions: 0
  Unit cell: (74.52, 69.12, 79.92, 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       7     16.00
     O     552      8.00
     N     489      7.00
     C    2175      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.01
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  752

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      87.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 40
      removed outlier: 4.147A  pdb=" N   HIS A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   CYS A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 67 through 90
      removed outlier: 4.010A  pdb=" N   VAL A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
    Processing helix  chain 'A' and resid 91 through 113
      removed outlier: 4.063A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.620A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 144
      removed outlier: 3.681A  pdb=" N   SER A 138 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 179
      removed outlier: 3.922A  pdb=" N   SER A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 203
      removed outlier: 3.616A  pdb=" N   ALA A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
      removed outlier: 3.714A  pdb=" N   ARG A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 296
      removed outlier: 4.090A  pdb=" N   ARG A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   TRP A 270 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER A 278 " --> pdb=" O   TRP A 274 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 327
      removed outlier: 3.680A  pdb=" N   GLY A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 327 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 356
      removed outlier: 3.548A  pdb=" N   THR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 391
      removed outlier: 3.710A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
      removed outlier: 4.683A  pdb=" N   SER A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   LEU A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 419
      removed outlier: 3.965A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN A 403 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 459
      removed outlier: 3.561A  pdb=" N   VAL A 437 " --> pdb=" O   GLN A 433 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)

    238 hydrogen bonds defined for protein.
    714 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 911
        1.35 -     1.46: 916
        1.46 -     1.58: 1491
        1.58 -     1.69: 4
        1.69 -     1.81: 11
  Bond restraints: 3333
  Sorted by residual:
  bond pdb=" C23 AJP A 703 "
       pdb=" C24 AJP A 703 "
    ideal  model  delta    sigma   weight residual
    1.522  1.610 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C23 AJP A 702 "
       pdb=" C24 AJP A 702 "
    ideal  model  delta    sigma   weight residual
    1.522  1.609 -0.087 2.00e-02 2.50e+03 1.91e+01
  bond pdb=" C05 AJP A 704 "
       pdb=" C06 AJP A 704 "
    ideal  model  delta    sigma   weight residual
    1.534  1.449  0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C23 AJP A 701 "
       pdb=" C24 AJP A 701 "
    ideal  model  delta    sigma   weight residual
    1.522  1.607 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C23 AJP A 704 "
       pdb=" C24 AJP A 704 "
    ideal  model  delta    sigma   weight residual
    1.522  1.606 -0.084 2.00e-02 2.50e+03 1.77e+01
  ... (remaining 3328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 4364
        1.38 -     2.75: 155
        2.75 -     4.13: 64
        4.13 -     5.51: 26
        5.51 -     6.88: 6
  Bond angle restraints: 4615
  Sorted by residual:
  angle pdb=" N   LEU A  80 "
        pdb=" CA  LEU A  80 "
        pdb=" C   LEU A  80 "
      ideal   model   delta    sigma   weight residual
     111.02  114.67   -3.65 1.22e+00 6.72e-01 8.95e+00
  angle pdb=" N   ILE A  41 "
        pdb=" CA  ILE A  41 "
        pdb=" C   ILE A  41 "
      ideal   model   delta    sigma   weight residual
     106.55  110.75   -4.20 1.45e+00 4.76e-01 8.40e+00
  angle pdb=" C   ILE A  41 "
        pdb=" CA  ILE A  41 "
        pdb=" CB  ILE A  41 "
      ideal   model   delta    sigma   weight residual
     112.68  109.72    2.96 1.14e+00 7.69e-01 6.74e+00
  angle pdb=" C07 AJP A 701 "
        pdb=" C06 AJP A 701 "
        pdb=" C83 AJP A 701 "
      ideal   model   delta    sigma   weight residual
     114.76  107.88    6.88 3.00e+00 1.11e-01 5.26e+00
  angle pdb=" N   PHE A 202 "
        pdb=" CA  PHE A 202 "
        pdb=" C   PHE A 202 "
      ideal   model   delta    sigma   weight residual
     111.82  114.30   -2.48 1.16e+00 7.43e-01 4.59e+00
  ... (remaining 4610 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.18: 2153
       32.18 -    64.37: 52
       64.37 -    96.55: 20
       96.55 -   128.73: 13
      128.73 -   160.91: 2
  Dihedral angle restraints: 2240
    sinusoidal: 1069
      harmonic: 1171
  Sorted by residual:
  dihedral pdb=" O31 AJP A 702 "
           pdb=" C30 AJP A 702 "
           pdb=" C32 AJP A 702 "
           pdb=" O33 AJP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.28  -21.81 -160.91     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C29 AJP A 702 "
           pdb=" C30 AJP A 702 "
           pdb=" C32 AJP A 702 "
           pdb=" O33 AJP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.96   98.67 -159.63     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C02 AJP A 703 "
           pdb=" C85 AJP A 703 "
           pdb=" O84 AJP A 703 "
           pdb=" C05 AJP A 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   62.65 -120.25     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 2237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 512
       0.070 -    0.140: 39
       0.140 -    0.210: 15
       0.210 -    0.280: 11
       0.280 -    0.350: 9
  Chirality restraints: 586
  Sorted by residual:
  chirality pdb=" C11 AJP A 702 "
            pdb=" C10 AJP A 702 "
            pdb=" C12 AJP A 702 "
            pdb=" C16 AJP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.55   -0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" C19 AJP A 702 "
            pdb=" C18 AJP A 702 "
            pdb=" C20 AJP A 702 "
            pdb=" C24 AJP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" C23 AJP A 703 "
            pdb=" C22 AJP A 703 "
            pdb=" C24 AJP A 703 "
            pdb=" O25 AJP A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.81    0.31 2.00e-01 2.50e+01 2.33e+00
  ... (remaining 583 not shown)

  Planarity restraints: 521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  93 "   -0.042 5.00e-02 4.00e+02   6.47e-02 6.70e+00
        pdb=" N   PRO A  94 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A  94 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  94 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "   -0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A  82 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO A  43 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.021 5.00e-02 4.00e+02
  ... (remaining 518 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 287
        2.74 -     3.28: 3597
        3.28 -     3.82: 5361
        3.82 -     4.36: 5566
        4.36 -     4.90: 9822
  Nonbonded interactions: 24633
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 135 "
            pdb=" OG  SER A 138 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O33 AJP A 701 "
            pdb=" O77 AJP A 701 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   LEU A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   GLN A 433 "
            pdb=" OG  SER A 436 "
     model   vdw
     2.410 3.040
  nonbonded pdb=" OE1 GLN A 172 "
            pdb=" OG1 THR A 176 "
     model   vdw
     2.424 3.040
  ... (remaining 24628 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.460
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     13.910
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
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      :  0.008   0.088   3333  Z= 0.401
  Angle     :  0.764   6.883   4615  Z= 0.347
  Chirality :  0.067   0.350    586
  Planarity :  0.005   0.065    521
  Dihedral  : 19.701 160.914   1488
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  8.09 %
    Favored  : 91.26 %
  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:  3.03 (0.41), residues: 394
  helix:  2.57 (0.27), residues: 317
  sheet:  None (None), residues: 0
  loop : -0.49 (0.73), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 118 
 PHE   0.008   0.001   PHE A 326 
 TYR   0.009   0.001   TYR A  35 
 ARG   0.001   0.000   ARG A 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15026 (  238)
  hydrogen bonds       : angle       5.61415 (  714)
  covalent geometry    : bond        0.00794 ( 3333)
  covalent geometry    : angle       0.76372 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8175 (tt0) cc_final: 0.7965 (tt0)
REVERT: A   75 SER cc_start: 0.9174 (m) cc_final: 0.8962 (t)
REVERT: A  287 TYR cc_start: 0.8052 (m-80) cc_final: 0.7788 (m-10)
REVERT: A  293 ASN cc_start: 0.8596 (t0) cc_final: 0.8333 (t0)
REVERT: A  294 GLU cc_start: 0.7821 (tp30) cc_final: 0.7316 (tp30)
REVERT: A  306 ASN cc_start: 0.8570 (m-40) cc_final: 0.8217 (t0)
REVERT: A  310 ASP cc_start: 0.9019 (t0) cc_final: 0.8749 (t70)
REVERT: A  316 LEU cc_start: 0.8900 (tp) cc_final: 0.8699 (tt)
REVERT: A  346 GLN cc_start: 0.8607 (mt0) cc_final: 0.8370 (mt0)
REVERT: A  361 SER cc_start: 0.8810 (m) cc_final: 0.8587 (t)
REVERT: A  412 THR cc_start: 0.8790 (m) cc_final: 0.8456 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1255
  time to fit residues: 18.4857
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.122208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.108386 restraints weight = 5622.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.111937 restraints weight = 2399.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.114248 restraints weight = 1319.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3333  Z= 0.152
  Angle     :  0.656   7.359   4615  Z= 0.305
  Chirality :  0.039   0.206    586
  Planarity :  0.004   0.052    521
  Dihedral  : 12.690 128.191    892
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.74 %
    Favored  : 77.02 %
  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:  3.65 (0.42), residues: 394
  helix:  2.87 (0.27), residues: 327
  sheet:  None (None), residues: 0
  loop : -0.02 (0.87), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.008   0.002   HIS A 355 
 PHE   0.023   0.001   PHE A 141 
 TYR   0.018   0.002   TYR A 149 
 ARG   0.001   0.000   ARG A 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05647 (  238)
  hydrogen bonds       : angle       4.28357 (  714)
  covalent geometry    : bond        0.00307 ( 3333)
  covalent geometry    : angle       0.65566 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8271 (tt0) cc_final: 0.8036 (tt0)
REVERT: A   75 SER cc_start: 0.9002 (m) cc_final: 0.8800 (t)
REVERT: A  123 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: A  181 SER cc_start: 0.8878 (m) cc_final: 0.8286 (p)
REVERT: A  293 ASN cc_start: 0.8570 (t0) cc_final: 0.8118 (t0)
REVERT: A  306 ASN cc_start: 0.8357 (m-40) cc_final: 0.7835 (t0)
REVERT: A  310 ASP cc_start: 0.9019 (t0) cc_final: 0.8776 (t70)
REVERT: A  316 LEU cc_start: 0.8774 (tp) cc_final: 0.8567 (tt)
REVERT: A  346 GLN cc_start: 0.8703 (mt0) cc_final: 0.8162 (mt0)
REVERT: A  361 SER cc_start: 0.8813 (m) cc_final: 0.8467 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 106
  average time/residue: 0.1313
  time to fit residues: 17.1936
Evaluate side-chains
  97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.121416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.107261 restraints weight = 5650.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.110815 restraints weight = 2438.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113193 restraints weight = 1354.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3333  Z= 0.147
  Angle     :  0.609   6.556   4615  Z= 0.287
  Chirality :  0.036   0.173    586
  Planarity :  0.004   0.048    521
  Dihedral  : 10.528 124.543    892
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 24.60 %
    Favored  : 72.49 %
  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:  3.70 (0.43), residues: 394
  helix:  2.99 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.26 (0.84), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A  27 
 PHE   0.014   0.001   PHE A 141 
 TYR   0.020   0.002   TYR A 287 
 ARG   0.005   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04818 (  238)
  hydrogen bonds       : angle       3.96757 (  714)
  covalent geometry    : bond        0.00314 ( 3333)
  covalent geometry    : angle       0.60921 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8313 (tt0) cc_final: 0.8054 (tt0)
REVERT: A  123 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8112 (mm-30)
REVERT: A  181 SER cc_start: 0.8844 (m) cc_final: 0.8263 (p)
REVERT: A  277 ASN cc_start: 0.8746 (m-40) cc_final: 0.8437 (m-40)
REVERT: A  287 TYR cc_start: 0.7958 (m-10) cc_final: 0.7747 (m-10)
REVERT: A  293 ASN cc_start: 0.8497 (t0) cc_final: 0.8216 (t0)
REVERT: A  294 GLU cc_start: 0.7758 (tp30) cc_final: 0.7546 (tp30)
REVERT: A  306 ASN cc_start: 0.8453 (m-40) cc_final: 0.7910 (t0)
REVERT: A  310 ASP cc_start: 0.9139 (t0) cc_final: 0.8832 (t70)
REVERT: A  346 GLN cc_start: 0.8683 (mt0) cc_final: 0.8180 (mt0)
REVERT: A  393 LYS cc_start: 0.8684 (tppt) cc_final: 0.8425 (tptp)
  outliers start: 9
  outliers final: 7
  residues processed: 93
  average time/residue: 0.1210
  time to fit residues: 14.1222
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  430 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 431 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.103228 restraints weight = 5725.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.106698 restraints weight = 2468.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.108897 restraints weight = 1350.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3333  Z= 0.184
  Angle     :  0.608   8.444   4615  Z= 0.296
  Chirality :  0.037   0.112    586
  Planarity :  0.004   0.046    521
  Dihedral  :  8.372 112.741    892
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 25.24 %
    Favored  : 69.90 %
  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:  3.25 (0.43), residues: 394
  helix:  2.65 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -0.32 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 107 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.010   0.001   PHE A 141 
 TYR   0.021   0.002   TYR A 435 
 ARG   0.007   0.001   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04974 (  238)
  hydrogen bonds       : angle       4.06223 (  714)
  covalent geometry    : bond        0.00398 ( 3333)
  covalent geometry    : angle       0.60830 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8382 (tt0) cc_final: 0.8106 (tt0)
REVERT: A  123 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8081 (mm-30)
REVERT: A  181 SER cc_start: 0.8937 (m) cc_final: 0.8393 (p)
REVERT: A  277 ASN cc_start: 0.8782 (m-40) cc_final: 0.8490 (m-40)
REVERT: A  287 TYR cc_start: 0.8162 (m-10) cc_final: 0.7550 (m-10)
REVERT: A  293 ASN cc_start: 0.8502 (t0) cc_final: 0.8048 (t0)
REVERT: A  294 GLU cc_start: 0.7908 (tp30) cc_final: 0.7553 (tp30)
REVERT: A  306 ASN cc_start: 0.8442 (m-40) cc_final: 0.7795 (t0)
REVERT: A  310 ASP cc_start: 0.9155 (t0) cc_final: 0.8844 (t0)
REVERT: A  313 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.9037 (p)
REVERT: A  346 GLN cc_start: 0.8716 (mt0) cc_final: 0.8215 (mt0)
REVERT: A  393 LYS cc_start: 0.8803 (tppt) cc_final: 0.8494 (tptp)
REVERT: A  412 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8850 (t)
  outliers start: 15
  outliers final: 8
  residues processed: 93
  average time/residue: 0.1232
  time to fit residues: 14.4520
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 431 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.105143 restraints weight = 5722.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.108557 restraints weight = 2446.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.110853 restraints weight = 1362.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3333  Z= 0.139
  Angle     :  0.579   8.652   4615  Z= 0.276
  Chirality :  0.035   0.168    586
  Planarity :  0.004   0.045    521
  Dihedral  :  6.161  55.365    892
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 25.89 %
    Favored  : 69.58 %
  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:  3.37 (0.43), residues: 394
  helix:  2.74 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.39 (0.81), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A  27 
 PHE   0.011   0.001   PHE A 141 
 TYR   0.022   0.002   TYR A 435 
 ARG   0.006   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04477 (  238)
  hydrogen bonds       : angle       3.87065 (  714)
  covalent geometry    : bond        0.00297 ( 3333)
  covalent geometry    : angle       0.57944 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8342 (tt0) cc_final: 0.8067 (tt0)
REVERT: A  123 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8075 (mm-30)
REVERT: A  277 ASN cc_start: 0.8758 (m-40) cc_final: 0.8537 (m-40)
REVERT: A  287 TYR cc_start: 0.8083 (m-10) cc_final: 0.7785 (m-10)
REVERT: A  293 ASN cc_start: 0.8469 (t0) cc_final: 0.8051 (t0)
REVERT: A  294 GLU cc_start: 0.7837 (tp30) cc_final: 0.7486 (tp30)
REVERT: A  306 ASN cc_start: 0.8491 (m-40) cc_final: 0.7920 (t0)
REVERT: A  310 ASP cc_start: 0.9131 (t0) cc_final: 0.8842 (t0)
REVERT: A  313 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9032 (p)
REVERT: A  412 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8773 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 91
  average time/residue: 0.1263
  time to fit residues: 14.5876
Evaluate side-chains
  88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0010
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.5386

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.120679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106431 restraints weight = 5762.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.110058 restraints weight = 2417.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112492 restraints weight = 1314.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3333  Z= 0.122
  Angle     :  0.582   8.239   4615  Z= 0.272
  Chirality :  0.034   0.112    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.403  55.605    892
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 27.83 %
    Favored  : 68.61 %
  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:  3.42 (0.43), residues: 394
  helix:  2.82 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.61 (0.78), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A  27 
 PHE   0.007   0.001   PHE A  59 
 TYR   0.022   0.002   TYR A 366 
 ARG   0.005   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  238)
  hydrogen bonds       : angle       3.76249 (  714)
  covalent geometry    : bond        0.00257 ( 3333)
  covalent geometry    : angle       0.58216 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8352 (tt0) cc_final: 0.8086 (tt0)
REVERT: A  123 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8100 (mm-30)
REVERT: A  277 ASN cc_start: 0.8682 (m-40) cc_final: 0.8448 (m110)
REVERT: A  287 TYR cc_start: 0.8059 (m-10) cc_final: 0.7717 (m-10)
REVERT: A  293 ASN cc_start: 0.8385 (t0) cc_final: 0.8156 (t0)
REVERT: A  294 GLU cc_start: 0.7779 (tp30) cc_final: 0.7578 (tp30)
REVERT: A  306 ASN cc_start: 0.8436 (m-40) cc_final: 0.7861 (t0)
REVERT: A  310 ASP cc_start: 0.9115 (t0) cc_final: 0.8837 (t0)
REVERT: A  313 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9028 (p)
REVERT: A  412 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1158
  time to fit residues: 12.8291
Evaluate side-chains
  88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.118941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.105404 restraints weight = 5695.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.108826 restraints weight = 2413.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.110984 restraints weight = 1321.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3333  Z= 0.143
  Angle     :  0.586   7.392   4615  Z= 0.278
  Chirality :  0.035   0.114    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.422  54.994    892
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 28.48 %
    Favored  : 67.96 %
  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:  3.32 (0.43), residues: 394
  helix:  2.75 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.69 (0.76), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 363 
 HIS   0.003   0.001   HIS A  27 
 PHE   0.008   0.001   PHE A 141 
 TYR   0.029   0.002   TYR A 149 
 ARG   0.006   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04313 (  238)
  hydrogen bonds       : angle       3.84824 (  714)
  covalent geometry    : bond        0.00309 ( 3333)
  covalent geometry    : angle       0.58605 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8366 (tt0) cc_final: 0.8113 (tt0)
REVERT: A  123 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8122 (mm-30)
REVERT: A  149 TYR cc_start: 0.8148 (t80) cc_final: 0.7787 (t80)
REVERT: A  287 TYR cc_start: 0.8154 (m-10) cc_final: 0.7794 (m-10)
REVERT: A  293 ASN cc_start: 0.8421 (t0) cc_final: 0.8050 (t0)
REVERT: A  294 GLU cc_start: 0.7859 (tp30) cc_final: 0.7533 (tp30)
REVERT: A  306 ASN cc_start: 0.8434 (m-40) cc_final: 0.7837 (t0)
REVERT: A  310 ASP cc_start: 0.9137 (t0) cc_final: 0.8837 (t0)
REVERT: A  313 SER cc_start: 0.9338 (OUTLIER) cc_final: 0.9045 (p)
REVERT: A  393 LYS cc_start: 0.8636 (tppt) cc_final: 0.8293 (tppt)
REVERT: A  412 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8796 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1142
  time to fit residues: 12.4692
Evaluate side-chains
  89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   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 = 0.3431 r_free = 0.3431 target = 0.119634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.105956 restraints weight = 5637.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.109365 restraints weight = 2398.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.111510 restraints weight = 1316.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3333  Z= 0.135
  Angle     :  0.587   9.308   4615  Z= 0.277
  Chirality :  0.035   0.112    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.385  55.075    892
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 28.80 %
    Favored  : 67.96 %
  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:  3.28 (0.43), residues: 394
  helix:  2.73 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.72 (0.76), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 363 
 HIS   0.003   0.001   HIS A  27 
 PHE   0.007   0.001   PHE A 276 
 TYR   0.023   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04165 (  238)
  hydrogen bonds       : angle       3.82836 (  714)
  covalent geometry    : bond        0.00296 ( 3333)
  covalent geometry    : angle       0.58746 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8356 (tt0) cc_final: 0.8104 (tt0)
REVERT: A  149 TYR cc_start: 0.8122 (t80) cc_final: 0.7758 (t80)
REVERT: A  287 TYR cc_start: 0.8129 (m-10) cc_final: 0.7758 (m-10)
REVERT: A  293 ASN cc_start: 0.8401 (t0) cc_final: 0.8027 (t0)
REVERT: A  294 GLU cc_start: 0.7855 (tp30) cc_final: 0.7514 (tp30)
REVERT: A  306 ASN cc_start: 0.8495 (m-40) cc_final: 0.7920 (t0)
REVERT: A  310 ASP cc_start: 0.9132 (t0) cc_final: 0.8834 (t0)
REVERT: A  313 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9045 (p)
REVERT: A  393 LYS cc_start: 0.8594 (tppt) cc_final: 0.8250 (tppt)
REVERT: A  412 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8779 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1243
  time to fit residues: 13.7819
Evaluate side-chains
  89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.117553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.103919 restraints weight = 5752.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.107301 restraints weight = 2440.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.109429 restraints weight = 1337.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3333  Z= 0.185
  Angle     :  0.635  10.720   4615  Z= 0.302
  Chirality :  0.037   0.161    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.529  54.437    892
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 28.16 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.06 (0.43), residues: 394
  helix:  2.61 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.83 (0.75), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 363 
 HIS   0.002   0.001   HIS A  27 
 PHE   0.009   0.001   PHE A 416 
 TYR   0.022   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04523 (  238)
  hydrogen bonds       : angle       4.00646 (  714)
  covalent geometry    : bond        0.00409 ( 3333)
  covalent geometry    : angle       0.63498 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8362 (tt0) cc_final: 0.8118 (tt0)
REVERT: A  122 MET cc_start: 0.8123 (tmm) cc_final: 0.7864 (tmm)
REVERT: A  149 TYR cc_start: 0.8145 (t80) cc_final: 0.7780 (t80)
REVERT: A  287 TYR cc_start: 0.8292 (m-10) cc_final: 0.7897 (m-10)
REVERT: A  293 ASN cc_start: 0.8466 (t0) cc_final: 0.8050 (t0)
REVERT: A  294 GLU cc_start: 0.7942 (tp30) cc_final: 0.7583 (tp30)
REVERT: A  306 ASN cc_start: 0.8446 (m-40) cc_final: 0.7848 (t0)
REVERT: A  310 ASP cc_start: 0.9092 (t0) cc_final: 0.8819 (t0)
REVERT: A  313 SER cc_start: 0.9366 (OUTLIER) cc_final: 0.9088 (p)
REVERT: A  393 LYS cc_start: 0.8634 (tppt) cc_final: 0.8295 (tppt)
  outliers start: 11
  outliers final: 9
  residues processed: 82
  average time/residue: 0.1187
  time to fit residues: 12.7129
Evaluate side-chains
  88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0870
   chunk 17 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.121322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.107674 restraints weight = 5538.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.111100 restraints weight = 2372.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.113374 restraints weight = 1307.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3333  Z= 0.123
  Angle     :  0.604   9.309   4615  Z= 0.281
  Chirality :  0.036   0.157    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.445  55.529    892
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 29.13 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.15 (0.43), residues: 394
  helix:  2.69 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.87 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 363 
 HIS   0.003   0.000   HIS A  27 
 PHE   0.006   0.001   PHE A 405 
 TYR   0.022   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 (  238)
  hydrogen bonds       : angle       3.82009 (  714)
  covalent geometry    : bond        0.00261 ( 3333)
  covalent geometry    : angle       0.60375 ( 4615)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8328 (tt0) cc_final: 0.8062 (tt0)
REVERT: A   77 LEU cc_start: 0.9327 (tp) cc_final: 0.9091 (tp)
REVERT: A  122 MET cc_start: 0.7943 (tmm) cc_final: 0.7655 (tmm)
REVERT: A  149 TYR cc_start: 0.8145 (t80) cc_final: 0.7806 (t80)
REVERT: A  287 TYR cc_start: 0.8130 (m-10) cc_final: 0.7725 (m-10)
REVERT: A  293 ASN cc_start: 0.8368 (t0) cc_final: 0.7988 (t0)
REVERT: A  294 GLU cc_start: 0.7835 (tp30) cc_final: 0.7466 (tp30)
REVERT: A  306 ASN cc_start: 0.8485 (m-40) cc_final: 0.7915 (t0)
REVERT: A  310 ASP cc_start: 0.9129 (t0) cc_final: 0.8827 (t0)
REVERT: A  313 SER cc_start: 0.9338 (OUTLIER) cc_final: 0.9063 (p)
REVERT: A  393 LYS cc_start: 0.8522 (tppt) cc_final: 0.8231 (tppt)
  outliers start: 8
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0990
  time to fit residues: 11.3378
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    0.1980
   chunk 10 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.122139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.108416 restraints weight = 5575.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.111981 restraints weight = 2369.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.114263 restraints weight = 1283.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3333  Z= 0.121
  Angle     :  0.608   9.640   4615  Z= 0.277
  Chirality :  0.035   0.140    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.320  55.237    892
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 30.10 %
    Favored  : 67.64 %
  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:  3.13 (0.43), residues: 394
  helix:  2.68 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.92 (0.72), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 363 
 HIS   0.003   0.000   HIS A  27 
 PHE   0.006   0.001   PHE A 103 
 TYR   0.026   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  238)
  hydrogen bonds       : angle       3.80904 (  714)
  covalent geometry    : bond        0.00257 ( 3333)
  covalent geometry    : angle       0.60800 ( 4615)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1252.56 seconds
wall clock time: 22 minutes 40.75 seconds (1360.75 seconds total)