Starting phenix.real_space_refine
on Fri May  9 20:30:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sc2_40335/05_2025/8sc2_40335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sc2_40335/05_2025/8sc2_40335.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sc2_40335/05_2025/8sc2_40335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sc2_40335/05_2025/8sc2_40335.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sc2_40335/05_2025/8sc2_40335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sc2_40335/05_2025/8sc2_40335.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.018
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      32      5.16       5
     C    2330      2.51       5
     N     572      2.21       5
     O     600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 3534
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3505
          Classifications: {'peptide': 453}
          Link IDs: {'PTRANS': 24, 'TRANS': 428}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'C9F': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.78, per 1000 atoms: 0.79
  Number of scatterers: 3534
  At special positions: 0
  Unit cell: (88.2, 82.32, 66.36, 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      32     16.00
     O     600      8.00
     N     572      7.00
     C    2330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 403.1 milliseconds
  

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  830

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 2 sheets defined
      82.1% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 31
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 54 through 63
    Processing helix  chain 'A' and resid 65 through 73
      removed outlier: 3.786A  pdb=" N   ASN A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 141 through 145
    Processing helix  chain 'A' and resid 146 through 173
      removed outlier: 4.064A  pdb=" N   LEU A 150 " --> pdb=" O   TRP A 146 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLN A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   GLY A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   TYR A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 194
      removed outlier: 3.848A  pdb=" N   ALA A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 228
      removed outlier: 3.712A  pdb=" N   VAL A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   VAL A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 232 through 258
      removed outlier: 3.604A  pdb=" N   VAL A 236 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   THR A 245 " --> pdb=" O   GLN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 279
      Proline residue:  A 271  - end of helix
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 4.479A  pdb=" N   THR A 340 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 372
    Processing helix  chain 'A' and resid 374 through 385
      removed outlier: 3.503A  pdb=" N   VAL A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 401
      removed outlier: 4.025A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG A 399 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY A 401 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 420
    Processing helix  chain 'A' and resid 427 through 457
      removed outlier: 3.668A  pdb=" N   ILE A 433 " --> pdb=" O   TRP A 429 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASN A 453 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   ALA A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   GLU A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 456 " --> pdb=" O   VAL A 452 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR A 457 " --> pdb=" O   ASN A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 491
      removed outlier: 3.962A  pdb=" N   LEU A 472 " --> pdb=" O   VAL A 468 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   CYS A 473 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASP A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
      removed outlier: 3.552A  pdb=" N   LEU A 487 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG A 488 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLU A 489 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL A 490 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 510
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91

    240 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 637
        1.33 -     1.45: 975
        1.45 -     1.58: 1970
        1.58 -     1.71: 0
        1.71 -     1.83: 48
  Bond restraints: 3630
  Sorted by residual:
  bond pdb=" N   ILE A 365 "
       pdb=" CA  ILE A 365 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.038 1.19e-02 7.06e+03 9.96e+00
  bond pdb=" N   VAL A  37 "
       pdb=" CA  VAL A  37 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.19e+00
  bond pdb=" N   LEU A 248 "
       pdb=" CA  LEU A 248 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 7.04e+00
  bond pdb=" N   LEU A 251 "
       pdb=" CA  LEU A 251 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.63e+00
  bond pdb=" N   TRP A  64 "
       pdb=" CA  TRP A  64 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.24e-02 6.50e+03 5.82e+00
  ... (remaining 3625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 4713
        1.07 -     2.14: 177
        2.14 -     3.20: 44
        3.20 -     4.27: 12
        4.27 -     5.34: 5
  Bond angle restraints: 4951
  Sorted by residual:
  angle pdb=" CA  ILE A 365 "
        pdb=" C   ILE A 365 "
        pdb=" O   ILE A 365 "
      ideal   model   delta    sigma   weight residual
     120.95  117.51    3.44 1.04e+00 9.25e-01 1.10e+01
  angle pdb=" CA  CYS A  36 "
        pdb=" C   CYS A  36 "
        pdb=" O   CYS A  36 "
      ideal   model   delta    sigma   weight residual
     120.70  117.45    3.25 1.03e+00 9.43e-01 9.93e+00
  angle pdb=" CA  VAL A  40 "
        pdb=" C   VAL A  40 "
        pdb=" O   VAL A  40 "
      ideal   model   delta    sigma   weight residual
     120.57  117.59    2.98 1.07e+00 8.73e-01 7.78e+00
  angle pdb=" C   GLU A 386 "
        pdb=" N   ILE A 387 "
        pdb=" CA  ILE A 387 "
      ideal   model   delta    sigma   weight residual
     120.33  122.52   -2.19 8.00e-01 1.56e+00 7.49e+00
  angle pdb=" N   ASP A 149 "
        pdb=" CA  ASP A 149 "
        pdb=" C   ASP A 149 "
      ideal   model   delta    sigma   weight residual
     111.71  108.79    2.92 1.15e+00 7.56e-01 6.43e+00
  ... (remaining 4946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.24: 1889
        9.24 -    18.49: 164
       18.49 -    27.73: 47
       27.73 -    36.98: 17
       36.98 -    46.22: 6
  Dihedral angle restraints: 2123
    sinusoidal: 826
      harmonic: 1297
  Sorted by residual:
  dihedral pdb=" N   LEU A 192 "
           pdb=" CA  LEU A 192 "
           pdb=" CB  LEU A 192 "
           pdb=" CG  LEU A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.37   41.37     3      1.50e+01 4.44e-03 7.40e+00
  dihedral pdb=" N   GLN A 241 "
           pdb=" CA  GLN A 241 "
           pdb=" CB  GLN A 241 "
           pdb=" CG  GLN A 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -140.11  -39.89     3      1.50e+01 4.44e-03 7.09e+00
  dihedral pdb=" C   ILE A 365 "
           pdb=" N   ILE A 365 "
           pdb=" CA  ILE A 365 "
           pdb=" CB  ILE A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -128.63    6.63     0      2.50e+00 1.60e-01 7.04e+00
  ... (remaining 2120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 447
       0.044 -    0.087: 93
       0.087 -    0.130: 26
       0.130 -    0.174: 3
       0.174 -    0.217: 2
  Chirality restraints: 571
  Sorted by residual:
  chirality pdb=" CA  ILE A  35 "
            pdb=" N   ILE A  35 "
            pdb=" C   ILE A  35 "
            pdb=" CB  ILE A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  LEU A 248 "
            pdb=" N   LEU A 248 "
            pdb=" C   LEU A 248 "
            pdb=" CB  LEU A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.56e-01
  chirality pdb=" CB  ILE A  35 "
            pdb=" CA  ILE A  35 "
            pdb=" CG1 ILE A  35 "
            pdb=" CG2 ILE A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.12e-01
  ... (remaining 568 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  40 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.39e+00
        pdb=" C   VAL A  40 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   VAL A  40 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE A  41 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 196 "    0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO A 197 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 197 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 197 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 258 "   -0.019 5.00e-02 4.00e+02   2.93e-02 1.37e+00
        pdb=" N   PRO A 259 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 259 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 259 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 839
        2.79 -     3.31: 3487
        3.31 -     3.84: 5626
        3.84 -     4.37: 6374
        4.37 -     4.90: 11282
  Nonbonded interactions: 27608
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 198 "
            pdb=" OG  SER A 201 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ILE A 392 "
            pdb=" OG1 THR A 396 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   GLY A 476 "
            pdb=" OG1 THR A 480 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   GLN A 209 "
            pdb=" OG  SER A 213 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   CYS A 142 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.360 3.040
  ... (remaining 27603 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.700
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
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      :  0.003   0.038   3633  Z= 0.201
  Angle     :  0.554   5.341   4957  Z= 0.346
  Chirality :  0.041   0.217    571
  Planarity :  0.004   0.036    612
  Dihedral  :  8.521  46.221   1284
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.42), residues: 449
  helix:  2.07 (0.31), residues: 311
  sheet:  None (None), residues: 0
  loop :  1.57 (0.60), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 261 
 HIS   0.001   0.000   HIS A  49 
 PHE   0.009   0.001   PHE A 355 
 TYR   0.007   0.001   TYR A 168 
 ARG   0.002   0.000   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14429 (  240)
  hydrogen bonds       : angle       5.37936 (  699)
  SS BOND              : bond        0.00184 (    3)
  SS BOND              : angle       1.63468 (    6)
  covalent geometry    : bond        0.00315 ( 3630)
  covalent geometry    : angle       0.55146 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.8480 (tpt) cc_final: 0.8139 (tpt)
REVERT: A  431 ASN cc_start: 0.8059 (t0) cc_final: 0.7805 (t0)
REVERT: A  435 MET cc_start: 0.8132 (tpp) cc_final: 0.7737 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1612
  time to fit residues: 21.3758
Evaluate side-chains
  83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 367 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.191256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.149527 restraints weight = 4660.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.35
r_work: 0.3511 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3633  Z= 0.134
  Angle     :  0.575   7.853   4957  Z= 0.288
  Chirality :  0.040   0.214    571
  Planarity :  0.004   0.037    612
  Dihedral  :  4.259  28.936    516
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.02 %
    Favored  : 89.12 %
  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:  2.88 (0.42), residues: 449
  helix:  2.12 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop :  1.66 (0.60), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.015   0.001   PHE A 334 
 TYR   0.013   0.001   TYR A  72 
 ARG   0.005   0.001   ARG A 486 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  240)
  hydrogen bonds       : angle       4.26511 (  699)
  SS BOND              : bond        0.00118 (    3)
  SS BOND              : angle       2.11482 (    6)
  covalent geometry    : bond        0.00296 ( 3630)
  covalent geometry    : angle       0.57101 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7831 (t0)
REVERT: A  431 ASN cc_start: 0.8123 (t0) cc_final: 0.7799 (t0)
REVERT: A  435 MET cc_start: 0.8048 (tpp) cc_final: 0.7654 (tpp)
REVERT: A  498 LEU cc_start: 0.7867 (tt) cc_final: 0.7408 (mm)
  outliers start: 7
  outliers final: 4
  residues processed: 92
  average time/residue: 0.1285
  time to fit residues: 15.0257
Evaluate side-chains
  85 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  467 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   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 = 0.4133 r_free = 0.4133 target = 0.189029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148291 restraints weight = 4661.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.53
r_work: 0.3494 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3633  Z= 0.135
  Angle     :  0.564   6.426   4957  Z= 0.281
  Chirality :  0.040   0.184    571
  Planarity :  0.004   0.031    612
  Dihedral  :  4.355  34.115    516
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.41 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.42), residues: 449
  helix:  2.05 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop :  1.57 (0.60), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 261 
 HIS   0.002   0.000   HIS A  49 
 PHE   0.010   0.001   PHE A  32 
 TYR   0.012   0.001   TYR A  72 
 ARG   0.003   0.000   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03990 (  240)
  hydrogen bonds       : angle       4.16113 (  699)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       1.90757 (    6)
  covalent geometry    : bond        0.00308 ( 3630)
  covalent geometry    : angle       0.55994 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: A  284 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6166 (mt-10)
REVERT: A  435 MET cc_start: 0.8074 (tpp) cc_final: 0.7686 (tpp)
REVERT: A  479 ILE cc_start: 0.6839 (mm) cc_final: 0.6579 (mt)
  outliers start: 9
  outliers final: 7
  residues processed: 86
  average time/residue: 0.1341
  time to fit residues: 14.5785
Evaluate side-chains
  84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0060
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0030
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0070
   chunk 44 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.3424

-------------------------------------------------------------------------------
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 = 0.4158 r_free = 0.4158 target = 0.191570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.150302 restraints weight = 4774.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.76
r_work: 0.3517 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3633  Z= 0.102
  Angle     :  0.512   9.034   4957  Z= 0.253
  Chirality :  0.038   0.198    571
  Planarity :  0.004   0.029    612
  Dihedral  :  4.228  35.294    516
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 11.41 %
    Favored  : 85.94 %
  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:  2.90 (0.42), residues: 449
  helix:  2.18 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop :  1.55 (0.60), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 354 
 HIS   0.002   0.000   HIS A  49 
 PHE   0.008   0.001   PHE A 355 
 TYR   0.011   0.001   TYR A  72 
 ARG   0.003   0.000   ARG A 486 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (  240)
  hydrogen bonds       : angle       3.94629 (  699)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       1.63222 (    6)
  covalent geometry    : bond        0.00209 ( 3630)
  covalent geometry    : angle       0.50918 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9083 (t0) cc_final: 0.8847 (t0)
REVERT: A  122 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8226 (tm-30)
REVERT: A  431 ASN cc_start: 0.8073 (t0) cc_final: 0.7725 (t0)
REVERT: A  435 MET cc_start: 0.8005 (tpp) cc_final: 0.7610 (tpp)
REVERT: A  448 MET cc_start: 0.8449 (mmm) cc_final: 0.8012 (mmm)
REVERT: A  479 ILE cc_start: 0.6622 (mm) cc_final: 0.6416 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 90
  average time/residue: 0.1284
  time to fit residues: 14.7397
Evaluate side-chains
  84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 6 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.190034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.148648 restraints weight = 4801.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.80
r_work: 0.3498 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3633  Z= 0.115
  Angle     :  0.546   9.219   4957  Z= 0.263
  Chirality :  0.039   0.199    571
  Planarity :  0.004   0.031    612
  Dihedral  :  4.259  34.304    516
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.47 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.42), residues: 449
  helix:  2.19 (0.31), residues: 313
  sheet:  None (None), residues: 0
  loop :  1.53 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 261 
 HIS   0.002   0.000   HIS A  49 
 PHE   0.015   0.001   PHE A 334 
 TYR   0.008   0.001   TYR A  91 
 ARG   0.002   0.000   ARG A 486 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  240)
  hydrogen bonds       : angle       3.99120 (  699)
  SS BOND              : bond        0.00192 (    3)
  SS BOND              : angle       1.71007 (    6)
  covalent geometry    : bond        0.00258 ( 3630)
  covalent geometry    : angle       0.54267 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6906 (ptt90)
REVERT: A   94 ASP cc_start: 0.9139 (t0) cc_final: 0.8871 (t0)
REVERT: A  431 ASN cc_start: 0.8086 (t0) cc_final: 0.7751 (t0)
REVERT: A  435 MET cc_start: 0.8004 (tpp) cc_final: 0.7618 (tpp)
REVERT: A  448 MET cc_start: 0.8487 (mmm) cc_final: 0.8004 (mmm)
REVERT: A  498 LEU cc_start: 0.7902 (tt) cc_final: 0.7335 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1474
  time to fit residues: 16.1656
Evaluate side-chains
  87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 33 optimal weight:    0.5980
   chunk 9 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.190805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.148950 restraints weight = 4788.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.80
r_work: 0.3494 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
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      :  0.002   0.025   3633  Z= 0.112
  Angle     :  0.536   9.393   4957  Z= 0.259
  Chirality :  0.040   0.266    571
  Planarity :  0.004   0.031    612
  Dihedral  :  4.181  35.105    516
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.12 %
    Favored  : 82.76 %
  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:  2.96 (0.42), residues: 449
  helix:  2.25 (0.31), residues: 313
  sheet:  None (None), residues: 0
  loop :  1.50 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.000   HIS A  49 
 PHE   0.008   0.001   PHE A 355 
 TYR   0.012   0.001   TYR A  72 
 ARG   0.002   0.000   ARG A 486 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (  240)
  hydrogen bonds       : angle       3.94601 (  699)
  SS BOND              : bond        0.00187 (    3)
  SS BOND              : angle       1.68474 (    6)
  covalent geometry    : bond        0.00249 ( 3630)
  covalent geometry    : angle       0.53301 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.7400 (ptt180) cc_final: 0.7032 (ptt90)
REVERT: A   94 ASP cc_start: 0.9159 (t0) cc_final: 0.8891 (t0)
REVERT: A  431 ASN cc_start: 0.8094 (t0) cc_final: 0.7759 (t0)
REVERT: A  435 MET cc_start: 0.8019 (tpp) cc_final: 0.7637 (tpp)
REVERT: A  448 MET cc_start: 0.8457 (mmm) cc_final: 0.7997 (mmm)
REVERT: A  472 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8068 (mm)
REVERT: A  498 LEU cc_start: 0.7937 (tt) cc_final: 0.7342 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 83
  average time/residue: 0.1586
  time to fit residues: 16.3757
Evaluate side-chains
  83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0670
   chunk 33 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.9522

-------------------------------------------------------------------------------
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 = 0.4132 r_free = 0.4132 target = 0.188665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.146603 restraints weight = 4708.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.70
r_work: 0.3475 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3633  Z= 0.145
  Angle     :  0.586   9.056   4957  Z= 0.283
  Chirality :  0.041   0.238    571
  Planarity :  0.004   0.034    612
  Dihedral  :  4.234  30.906    516
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.92 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.42), residues: 449
  helix:  2.08 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop :  1.49 (0.59), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.010   0.001   PHE A  32 
 TYR   0.009   0.001   TYR A  91 
 ARG   0.002   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  240)
  hydrogen bonds       : angle       4.14924 (  699)
  SS BOND              : bond        0.00250 (    3)
  SS BOND              : angle       1.82176 (    6)
  covalent geometry    : bond        0.00342 ( 3630)
  covalent geometry    : angle       0.58252 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9163 (t0) cc_final: 0.8910 (t0)
REVERT: A  123 ASP cc_start: 0.8311 (m-30) cc_final: 0.8076 (m-30)
REVERT: A  239 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7782 (mpp)
REVERT: A  435 MET cc_start: 0.8073 (tpp) cc_final: 0.7721 (tpp)
REVERT: A  448 MET cc_start: 0.8484 (mmm) cc_final: 0.8054 (mmm)
REVERT: A  472 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8062 (mm)
REVERT: A  498 LEU cc_start: 0.7969 (tt) cc_final: 0.7370 (mm)
  outliers start: 11
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1216
  time to fit residues: 13.0965
Evaluate side-chains
  87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    0.2980
   chunk 4 optimal weight:    9.9990
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4143 r_free = 0.4143 target = 0.190114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149325 restraints weight = 4677.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.33
r_work: 0.3501 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3633  Z= 0.115
  Angle     :  0.563   9.221   4957  Z= 0.272
  Chirality :  0.040   0.218    571
  Planarity :  0.004   0.031    612
  Dihedral  :  4.180  33.922    516
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.71 %
    Favored  : 81.17 %
  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:  2.84 (0.42), residues: 449
  helix:  2.15 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop :  1.47 (0.59), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.009   0.001   PHE A 355 
 TYR   0.012   0.001   TYR A  72 
 ARG   0.005   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (  240)
  hydrogen bonds       : angle       4.07628 (  699)
  SS BOND              : bond        0.00181 (    3)
  SS BOND              : angle       1.73579 (    6)
  covalent geometry    : bond        0.00258 ( 3630)
  covalent geometry    : angle       0.56041 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9167 (t0) cc_final: 0.8912 (t0)
REVERT: A  239 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7736 (mpp)
REVERT: A  431 ASN cc_start: 0.8097 (t0) cc_final: 0.7770 (t0)
REVERT: A  435 MET cc_start: 0.8060 (tpp) cc_final: 0.7676 (tpp)
REVERT: A  448 MET cc_start: 0.8477 (mmm) cc_final: 0.8014 (mmm)
REVERT: A  472 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8045 (mm)
REVERT: A  498 LEU cc_start: 0.7929 (tt) cc_final: 0.7347 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 81
  average time/residue: 0.1459
  time to fit residues: 14.8594
Evaluate side-chains
  86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.189094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.147591 restraints weight = 4704.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.61
r_work: 0.3492 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3633  Z= 0.129
  Angle     :  0.569   9.455   4957  Z= 0.278
  Chirality :  0.040   0.219    571
  Planarity :  0.004   0.032    612
  Dihedral  :  4.228  31.471    516
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.18 %
    Favored  : 81.17 %
  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:  2.78 (0.42), residues: 449
  helix:  2.09 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop :  1.46 (0.59), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.009   0.001   PHE A 355 
 TYR   0.011   0.001   TYR A  91 
 ARG   0.002   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (  240)
  hydrogen bonds       : angle       4.12857 (  699)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       1.80877 (    6)
  covalent geometry    : bond        0.00298 ( 3630)
  covalent geometry    : angle       0.56543 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9178 (t0) cc_final: 0.8930 (t0)
REVERT: A  239 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7764 (mpp)
REVERT: A  435 MET cc_start: 0.8077 (tpp) cc_final: 0.7696 (tpp)
REVERT: A  448 MET cc_start: 0.8490 (mmm) cc_final: 0.8038 (mmm)
REVERT: A  472 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8054 (mm)
REVERT: A  498 LEU cc_start: 0.7942 (tt) cc_final: 0.7347 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 81
  average time/residue: 0.1300
  time to fit residues: 13.5482
Evaluate side-chains
  83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.188627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.146665 restraints weight = 4725.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.73
r_work: 0.3473 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3633  Z= 0.136
  Angle     :  0.591   9.421   4957  Z= 0.289
  Chirality :  0.041   0.222    571
  Planarity :  0.004   0.032    612
  Dihedral  :  4.207  30.268    516
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.51 %
    Favored  : 80.37 %
  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:  2.70 (0.42), residues: 449
  helix:  2.05 (0.30), residues: 314
  sheet: -0.47 (1.42), residues: 10
  loop :  1.56 (0.63), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.009   0.001   PHE A 355 
 TYR   0.012   0.001   TYR A  72 
 ARG   0.002   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  240)
  hydrogen bonds       : angle       4.19498 (  699)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       1.78653 (    6)
  covalent geometry    : bond        0.00317 ( 3630)
  covalent geometry    : angle       0.58836 ( 4951)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9207 (t0) cc_final: 0.8951 (t0)
REVERT: A  239 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7783 (mpp)
REVERT: A  435 MET cc_start: 0.8048 (tpp) cc_final: 0.7678 (tpp)
REVERT: A  472 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8035 (mm)
REVERT: A  498 LEU cc_start: 0.7956 (tt) cc_final: 0.7355 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 81
  average time/residue: 0.1506
  time to fit residues: 15.4929
Evaluate side-chains
  85 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.3980
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.189169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.147561 restraints weight = 4709.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.74
r_work: 0.3476 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3633  Z= 0.127
  Angle     :  0.589   9.567   4957  Z= 0.288
  Chirality :  0.042   0.312    571
  Planarity :  0.004   0.031    612
  Dihedral  :  4.223  30.834    516
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.30 %
    Favored  : 79.58 %
  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:  2.68 (0.41), residues: 449
  helix:  2.04 (0.30), residues: 314
  sheet: -0.41 (1.43), residues: 10
  loop :  1.53 (0.62), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.009   0.001   PHE A 355 
 TYR   0.008   0.001   TYR A 352 
 ARG   0.001   0.000   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03691 (  240)
  hydrogen bonds       : angle       4.19321 (  699)
  SS BOND              : bond        0.00219 (    3)
  SS BOND              : angle       1.74193 (    6)
  covalent geometry    : bond        0.00290 ( 3630)
  covalent geometry    : angle       0.58574 ( 4951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2071.47 seconds
wall clock time: 36 minutes 27.68 seconds (2187.68 seconds total)