Starting phenix.real_space_refine
on Wed Mar  5 21:09:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dep_27394/03_2025/8dep_27394.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dep_27394/03_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_27394/03_2025/8dep_27394.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dep_27394/03_2025/8dep_27394.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dep_27394/03_2025/8dep_27394.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dep_27394/03_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-5624/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: 2.93, per 1000 atoms: 0.91
  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: 0.94
  Conformation dependent library (CDL) restraints added in 395.2 milliseconds
  

  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: 0.28
  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: 0.81

  Time building geometry restraints manager: 1.11 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:             0.440
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.210
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.820
-------------------------------------------------------------------------------
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= 0.472
  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 

*********************** 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  : 0.298 
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: 0.1268
  time to fit residues: 18.8644
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  : 0.309 
-------------------------------------------------------------------------------
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 = 0.122204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.108364 restraints weight = 5623.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.111808 restraints weight = 2402.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.114178 restraints weight = 1357.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2054

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= 0.202
  Angle     :  0.656   7.360   4615  Z= 0.305
  Chirality :  0.039   0.205    586
  Planarity :  0.004   0.052    521
  Dihedral  : 12.695 128.246    892
  Min Nonbonded Distance : 2.492

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  42 

*********************** 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  : 0.305 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8278 (tt0) cc_final: 0.8040 (tt0)
REVERT: A   75 SER cc_start: 0.8996 (m) cc_final: 0.8792 (t)
REVERT: A  123 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8063 (mm-30)
REVERT: A  181 SER cc_start: 0.8872 (m) cc_final: 0.8278 (p)
REVERT: A  293 ASN cc_start: 0.8566 (t0) cc_final: 0.8113 (t0)
REVERT: A  306 ASN cc_start: 0.8357 (m-40) cc_final: 0.7828 (t0)
REVERT: A  310 ASP cc_start: 0.9021 (t0) cc_final: 0.8777 (t70)
REVERT: A  316 LEU cc_start: 0.8762 (tp) cc_final: 0.8555 (tt)
REVERT: A  346 GLN cc_start: 0.8693 (mt0) cc_final: 0.8148 (mt0)
REVERT: A  361 SER cc_start: 0.8812 (m) cc_final: 0.8470 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 106
  average time/residue: 0.1312
  time to fit residues: 17.1063
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  : 0.303 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3465 r_free = 0.3465 target = 0.122017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.107698 restraints weight = 5660.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.111317 restraints weight = 2437.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.113662 restraints weight = 1349.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3333  Z= 0.188
  Angle     :  0.603   6.545   4615  Z= 0.283
  Chirality :  0.036   0.171    586
  Planarity :  0.004   0.048    521
  Dihedral  : 10.523 125.296    892
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 24.92 %
    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:  3.72 (0.43), residues: 394
  helix:  3.01 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.29 (0.84), residues: 72

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   0.014   0.001   PHE A 141 
 TYR   0.021   0.002   TYR A 287 
 ARG   0.005   0.001   ARG A  61 

*********************** 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
  103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8321 (tt0) cc_final: 0.8061 (tt0)
REVERT: A  123 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8105 (mm-30)
REVERT: A  172 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: A  181 SER cc_start: 0.8838 (m) cc_final: 0.8250 (p)
REVERT: A  277 ASN cc_start: 0.8717 (m-40) cc_final: 0.8422 (m-40)
REVERT: A  293 ASN cc_start: 0.8477 (t0) cc_final: 0.8211 (t0)
REVERT: A  294 GLU cc_start: 0.7713 (tp30) cc_final: 0.7497 (tp30)
REVERT: A  306 ASN cc_start: 0.8428 (m-40) cc_final: 0.7873 (t0)
REVERT: A  310 ASP cc_start: 0.9130 (t0) cc_final: 0.8823 (t70)
REVERT: A  346 GLN cc_start: 0.8661 (mt0) cc_final: 0.8169 (mt0)
REVERT: A  393 LYS cc_start: 0.8674 (tppt) cc_final: 0.8416 (tptp)
  outliers start: 8
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1231
  time to fit residues: 15.1836
Evaluate side-chains
  89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  194 THR
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:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 15 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 = 0.3443 r_free = 0.3443 target = 0.120477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.106463 restraints weight = 5606.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.110036 restraints weight = 2425.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.112289 restraints weight = 1334.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3093

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= 0.194
  Angle     :  0.564   7.588   4615  Z= 0.269
  Chirality :  0.034   0.111    586
  Planarity :  0.004   0.044    521
  Dihedral  :  8.190 112.497    892
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 26.54 %
    Favored  : 68.93 %
  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:  3.52 (0.43), residues: 394
  helix:  2.85 (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   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A  27 
 PHE   0.012   0.001   PHE A 141 
 TYR   0.015   0.002   TYR A 435 
 ARG   0.004   0.000   ARG A 133 

*********************** 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
  108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8312 (tt0) cc_final: 0.8013 (tt0)
REVERT: A  123 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: A  130 MET cc_start: 0.8481 (tpt) cc_final: 0.8174 (tpt)
REVERT: A  181 SER cc_start: 0.8898 (m) cc_final: 0.8341 (p)
REVERT: A  277 ASN cc_start: 0.8754 (m-40) cc_final: 0.8463 (m-40)
REVERT: A  287 TYR cc_start: 0.7833 (m-10) cc_final: 0.7558 (m-10)
REVERT: A  293 ASN cc_start: 0.8430 (t0) cc_final: 0.8015 (t0)
REVERT: A  294 GLU cc_start: 0.7758 (tp30) cc_final: 0.7396 (tp30)
REVERT: A  306 ASN cc_start: 0.8527 (m-40) cc_final: 0.7898 (t0)
REVERT: A  310 ASP cc_start: 0.9150 (t0) cc_final: 0.8840 (t0)
REVERT: A  346 GLN cc_start: 0.8689 (mt0) cc_final: 0.8179 (mt0)
REVERT: A  393 LYS cc_start: 0.8657 (tppt) cc_final: 0.8325 (tptp)
REVERT: A  412 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8830 (t)
  outliers start: 14
  outliers final: 7
  residues processed: 103
  average time/residue: 0.1208
  time to fit residues: 15.8164
Evaluate side-chains
  99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  380 VAL
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:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   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 266 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.120750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.106849 restraints weight = 5675.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.110400 restraints weight = 2437.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112729 restraints weight = 1338.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3333  Z= 0.186
  Angle     :  0.575   8.819   4615  Z= 0.272
  Chirality :  0.035   0.173    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.965  54.918    892
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.24
  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:  3.41 (0.43), residues: 394
  helix:  2.78 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.47 (0.81), 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   0.008   0.001   PHE A  59 
 TYR   0.015   0.002   TYR A 149 
 ARG   0.004   0.000   ARG A 133 

*********************** 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
  103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8303 (tt0) cc_final: 0.8016 (tt0)
REVERT: A  123 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8056 (mm-30)
REVERT: A  130 MET cc_start: 0.8466 (tpt) cc_final: 0.8144 (tpt)
REVERT: A  181 SER cc_start: 0.8891 (m) cc_final: 0.8309 (p)
REVERT: A  277 ASN cc_start: 0.8729 (m-40) cc_final: 0.8421 (m110)
REVERT: A  287 TYR cc_start: 0.7874 (m-10) cc_final: 0.7608 (m-10)
REVERT: A  293 ASN cc_start: 0.8404 (t0) cc_final: 0.8165 (t0)
REVERT: A  306 ASN cc_start: 0.8484 (m-40) cc_final: 0.7913 (t0)
REVERT: A  310 ASP cc_start: 0.9147 (t0) cc_final: 0.8864 (t0)
REVERT: A  313 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.9018 (p)
REVERT: A  411 LYS cc_start: 0.8755 (tttt) cc_final: 0.8445 (tttp)
REVERT: A  412 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8801 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 98
  average time/residue: 0.1230
  time to fit residues: 15.3135
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
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:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3421 r_free = 0.3421 target = 0.119001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.105100 restraints weight = 5856.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.108612 restraints weight = 2493.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.110825 restraints weight = 1371.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3595

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= 0.222
  Angle     :  0.575   7.467   4615  Z= 0.278
  Chirality :  0.035   0.114    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.451  54.610    892
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 27.51 %
    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:  3.34 (0.43), residues: 394
  helix:  2.72 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.46 (0.81), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A  27 
 PHE   0.012   0.001   PHE A  59 
 TYR   0.021   0.002   TYR A 149 
 ARG   0.006   0.000   ARG A 133 

*********************** 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: 14
    poor density    : 80
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8357 (tt0) cc_final: 0.8077 (tt0)
REVERT: A  130 MET cc_start: 0.8466 (tpt) cc_final: 0.8129 (tpt)
REVERT: A  277 ASN cc_start: 0.8727 (m-40) cc_final: 0.8472 (m110)
REVERT: A  287 TYR cc_start: 0.7942 (m-10) cc_final: 0.7616 (m-10)
REVERT: A  293 ASN cc_start: 0.8380 (t0) cc_final: 0.7918 (t0)
REVERT: A  294 GLU cc_start: 0.7868 (tp30) cc_final: 0.7169 (tp30)
REVERT: A  306 ASN cc_start: 0.8463 (m-40) cc_final: 0.7888 (t0)
REVERT: A  310 ASP cc_start: 0.9168 (t0) cc_final: 0.8871 (t0)
REVERT: A  313 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9038 (p)
REVERT: A  411 LYS cc_start: 0.8836 (tttt) cc_final: 0.8512 (tttp)
REVERT: A  412 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8832 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 88
  average time/residue: 0.1199
  time to fit residues: 13.5409
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  : 0.310 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0370
   chunk 32 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.4858

-------------------------------------------------------------------------------
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 = 0.121614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107653 restraints weight = 5575.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111203 restraints weight = 2374.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.113547 restraints weight = 1302.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3788

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= 0.167
  Angle     :  0.553   8.983   4615  Z= 0.265
  Chirality :  0.034   0.111    586
  Planarity :  0.004   0.044    521
  Dihedral  :  5.343  55.241    892
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 29.77 %
    Favored  : 66.67 %
  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:  3.17 (0.43), residues: 394
  helix:  2.68 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop : -0.80 (0.75), residues: 71

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   0.023   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 

*********************** 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
  97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8328 (tt0) cc_final: 0.8060 (tt0)
REVERT: A  130 MET cc_start: 0.8437 (tpt) cc_final: 0.8150 (tpt)
REVERT: A  277 ASN cc_start: 0.8659 (m-40) cc_final: 0.8427 (m110)
REVERT: A  287 TYR cc_start: 0.7788 (m-10) cc_final: 0.7430 (m-10)
REVERT: A  293 ASN cc_start: 0.8328 (t0) cc_final: 0.7880 (t0)
REVERT: A  294 GLU cc_start: 0.7805 (tp30) cc_final: 0.7152 (tp30)
REVERT: A  306 ASN cc_start: 0.8427 (m-40) cc_final: 0.7870 (t0)
REVERT: A  310 ASP cc_start: 0.9137 (t0) cc_final: 0.8859 (t0)
REVERT: A  313 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9030 (p)
REVERT: A  336 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7283 (mmtt)
REVERT: A  393 LYS cc_start: 0.8543 (tppt) cc_final: 0.8216 (tppt)
  outliers start: 11
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1128
  time to fit residues: 12.9794
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  336 LYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.120545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.106763 restraints weight = 5679.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.110252 restraints weight = 2398.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112569 restraints weight = 1311.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3925

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= 0.193
  Angle     :  0.548   8.264   4615  Z= 0.270
  Chirality :  0.034   0.125    586
  Planarity :  0.004   0.045    521
  Dihedral  :  5.334  54.711    892
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 30.74 %
    Favored  : 65.70 %
  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 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 363 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.006   0.001   PHE A 416 
 TYR   0.023   0.002   TYR A 149 
 ARG   0.006   0.000   ARG A 133 

*********************** 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
  96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8353 (tt0) cc_final: 0.8080 (tt0)
REVERT: A  123 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7670 (tm-30)
REVERT: A  130 MET cc_start: 0.8512 (tpt) cc_final: 0.8241 (tpt)
REVERT: A  141 PHE cc_start: 0.8829 (t80) cc_final: 0.8041 (t80)
REVERT: A  277 ASN cc_start: 0.8621 (m-40) cc_final: 0.8402 (m110)
REVERT: A  287 TYR cc_start: 0.7960 (m-10) cc_final: 0.7608 (m-10)
REVERT: A  293 ASN cc_start: 0.8352 (t0) cc_final: 0.7901 (t0)
REVERT: A  294 GLU cc_start: 0.7882 (tp30) cc_final: 0.7153 (tp30)
REVERT: A  306 ASN cc_start: 0.8477 (m-40) cc_final: 0.7928 (t0)
REVERT: A  310 ASP cc_start: 0.9126 (t0) cc_final: 0.8838 (t0)
REVERT: A  313 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.9043 (p)
REVERT: A  336 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7299 (mmtt)
REVERT: A  393 LYS cc_start: 0.8508 (tppt) cc_final: 0.8098 (tppt)
  outliers start: 11
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1186
  time to fit residues: 13.4915
Evaluate side-chains
  95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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  283 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  336 LYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.120904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.107102 restraints weight = 5711.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.110621 restraints weight = 2399.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.112947 restraints weight = 1308.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3333  Z= 0.186
  Angle     :  0.538   8.097   4615  Z= 0.266
  Chirality :  0.034   0.112    586
  Planarity :  0.004   0.045    521
  Dihedral  :  5.353  54.726    892
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 30.42 %
    Favored  : 65.37 %
  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:  3.09 (0.43), residues: 394
  helix:  2.66 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.95 (0.72), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 363 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.007   0.001   PHE A 416 
 TYR   0.022   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 

*********************** 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
  99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8341 (tt0) cc_final: 0.8069 (tt0)
REVERT: A  130 MET cc_start: 0.8572 (tpt) cc_final: 0.8362 (tpt)
REVERT: A  141 PHE cc_start: 0.8743 (t80) cc_final: 0.7928 (t80)
REVERT: A  277 ASN cc_start: 0.8658 (m-40) cc_final: 0.8416 (m110)
REVERT: A  287 TYR cc_start: 0.7939 (m-10) cc_final: 0.7539 (m-10)
REVERT: A  293 ASN cc_start: 0.8332 (t0) cc_final: 0.7914 (t0)
REVERT: A  294 GLU cc_start: 0.7872 (tp30) cc_final: 0.7173 (tp30)
REVERT: A  306 ASN cc_start: 0.8467 (m-40) cc_final: 0.7913 (t0)
REVERT: A  310 ASP cc_start: 0.9119 (t0) cc_final: 0.8835 (t0)
REVERT: A  313 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9058 (p)
REVERT: A  393 LYS cc_start: 0.8397 (tppt) cc_final: 0.8047 (tppt)
  outliers start: 13
  outliers final: 8
  residues processed: 91
  average time/residue: 0.1043
  time to fit residues: 12.4834
Evaluate side-chains
  95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
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:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.120083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.106707 restraints weight = 5587.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.110107 restraints weight = 2374.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112316 restraints weight = 1297.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3333  Z= 0.212
  Angle     :  0.573   8.057   4615  Z= 0.279
  Chirality :  0.035   0.114    586
  Planarity :  0.004   0.045    521
  Dihedral  :  5.362  54.295    892
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 29.13 %
    Favored  : 66.99 %
  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:  3.02 (0.43), residues: 394
  helix:  2.60 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.92 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 363 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.007   0.001   PHE A 141 
 TYR   0.026   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 

********************** 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
  99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8346 (tt0) cc_final: 0.8077 (tt0)
REVERT: A  123 GLU cc_start: 0.8019 (tp30) cc_final: 0.7598 (tm-30)
REVERT: A  125 PHE cc_start: 0.9037 (m-80) cc_final: 0.8836 (m-80)
REVERT: A  130 MET cc_start: 0.8598 (tpt) cc_final: 0.8396 (tpt)
REVERT: A  141 PHE cc_start: 0.8805 (t80) cc_final: 0.7716 (t80)
REVERT: A  287 TYR cc_start: 0.7900 (m-10) cc_final: 0.7545 (m-10)
REVERT: A  293 ASN cc_start: 0.8329 (t0) cc_final: 0.7940 (t0)
REVERT: A  294 GLU cc_start: 0.7887 (tp30) cc_final: 0.7162 (tp30)
REVERT: A  306 ASN cc_start: 0.8478 (m-40) cc_final: 0.7916 (t0)
REVERT: A  310 ASP cc_start: 0.9133 (t0) cc_final: 0.8829 (t0)
REVERT: A  313 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9056 (p)
REVERT: A  393 LYS cc_start: 0.8484 (tppt) cc_final: 0.8087 (tppt)
  outliers start: 12
  outliers final: 8
  residues processed: 93
  average time/residue: 0.1026
  time to fit residues: 12.6252
Evaluate side-chains
  94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  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 17 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0370
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0980
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.122482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.108800 restraints weight = 5601.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.112285 restraints weight = 2365.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.114466 restraints weight = 1295.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.4357

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= 0.170
  Angle     :  0.548   7.856   4615  Z= 0.267
  Chirality :  0.034   0.109    586
  Planarity :  0.004   0.045    521
  Dihedral  :  5.265  54.736    892
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 29.45 %
    Favored  : 67.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.43), residues: 394
  helix:  2.54 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.86 (0.72), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 270 
 HIS   0.002   0.000   HIS A  27 
 PHE   0.006   0.001   PHE A 276 
 TYR   0.030   0.002   TYR A 366 
 ARG   0.006   0.000   ARG A 133 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1250.16 seconds
wall clock time: 22 minutes 20.35 seconds (1340.35 seconds total)