Starting phenix.real_space_refine
on Fri May  9 15:11:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hhq_52173/05_2025/9hhq_52173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hhq_52173/05_2025/9hhq_52173.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hhq_52173/05_2025/9hhq_52173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hhq_52173/05_2025/9hhq_52173.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hhq_52173/05_2025/9hhq_52173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hhq_52173/05_2025/9hhq_52173.cif"
  }
  resolution = 3.5
  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=   0.001
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      30      5.16       5
     C    1897      2.51       5
     N     429      2.21       5
     O     462      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2818
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2818
          Classifications: {'peptide': 369}
          Link IDs: {'PTRANS': 15, 'TRANS': 353}
          Chain breaks: 1
  Time building chain proxies: 2.35, per 1000 atoms: 0.83
  Number of scatterers: 2818
  At special positions: 0
  Unit cell: (69.3066, 53.1667, 67.4077, 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      30     16.00
     O     462      8.00
     N     429      7.00
     C    1897      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: 0.69
  Conformation dependent library (CDL) restraints added in 350.2 milliseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  662

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      91.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 90
      removed outlier: 3.639A  pdb=" N   ILE A  87 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLN A  88 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 4.052A  pdb=" N   LEU A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 128
      removed outlier: 3.673A  pdb=" N   TRP A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   VAL A 117 " --> pdb=" O   LYS A 113 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   GLY A 118 " --> pdb=" O   THR A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 140
      removed outlier: 3.824A  pdb=" N   LEU A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY A 140 " --> pdb=" O   THR A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 160
      removed outlier: 3.607A  pdb=" N   SER A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 4.295A  pdb=" N   LEU A 170 " --> pdb=" O   GLU A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 191
      removed outlier: 3.571A  pdb=" N   GLN A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
      Proline residue:  A 186  - end of helix
      removed outlier: 3.873A  pdb=" N   LEU A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 229
      removed outlier: 3.534A  pdb=" N   VAL A 202 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
    Processing helix  chain 'A' and resid 230 through 247
      removed outlier: 3.615A  pdb=" N   CYS A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ILE A 239 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   PHE A 240 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 289
      removed outlier: 3.608A  pdb=" N   LYS A 289 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 304
      Proline residue:  A 301  - end of helix
    Processing helix  chain 'A' and resid 307 through 322
      removed outlier: 4.555A  pdb=" N   TYR A 311 " --> pdb=" O   TYR A 307 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   MET A 315 " --> pdb=" O   TYR A 311 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   LYS A 316 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
    Processing helix  chain 'A' and resid 350 through 353
      removed outlier: 3.724A  pdb=" N   VAL A 353 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 350 through 353'
    Processing helix  chain 'A' and resid 354 through 356
      No H-bonds generated for 'chain 'A' and resid 354 through 356'
    Processing helix  chain 'A' and resid 357 through 375
      removed outlier: 4.086A  pdb=" N   LEU A 361 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 402
    Processing helix  chain 'A' and resid 402 through 411
      removed outlier: 4.091A  pdb=" N   ILE A 406 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ALA A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 414
      No H-bonds generated for 'chain 'A' and resid 412 through 414'
    Processing helix  chain 'A' and resid 415 through 427
    Processing helix  chain 'A' and resid 427 through 446
      removed outlier: 3.525A  pdb=" N   MET A 431 " --> pdb=" O   MET A 427 " (cutoff:3.500A)
      Proline residue:  A 435  - end of helix
    Processing helix  chain 'A' and resid 448 through 456
    Processing helix  chain 'A' and resid 457 through 467
      removed outlier: 3.648A  pdb=" N   CYS A 467 " --> pdb=" O   GLY A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472

    208 hydrogen bonds defined for protein.
    615 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: 0.82

  Time building geometry restraints manager: 0.82 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: 821
        1.35 -     1.46: 719
        1.46 -     1.58: 1305
        1.58 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 2892
  Sorted by residual:
  bond pdb=" C   ALA A 404 "
       pdb=" N   PRO A 405 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 1.28e-02 6.10e+03 9.05e-01
  bond pdb=" C   PRO A 458 "
       pdb=" N   PRO A 459 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.28e-02 6.10e+03 7.86e-01
  bond pdb=" CB  PRO A 459 "
       pdb=" CG  PRO A 459 "
    ideal  model  delta    sigma   weight residual
    1.492  1.448  0.044 5.00e-02 4.00e+02 7.75e-01
  bond pdb=" CA  PRO A 458 "
       pdb=" C   PRO A 458 "
    ideal  model  delta    sigma   weight residual
    1.517  1.525 -0.008 9.30e-03 1.16e+04 7.39e-01
  bond pdb=" CA  LYS A 196 "
       pdb=" C   LYS A 196 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.34e-02 5.57e+03 7.39e-01
  ... (remaining 2887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 3832
        1.92 -     3.84: 66
        3.84 -     5.76: 17
        5.76 -     7.68: 7
        7.68 -     9.59: 1
  Bond angle restraints: 3923
  Sorted by residual:
  angle pdb=" N   PRO A 458 "
        pdb=" CA  PRO A 458 "
        pdb=" C   PRO A 458 "
      ideal   model   delta    sigma   weight residual
     110.70  114.70   -4.00 1.22e+00 6.72e-01 1.08e+01
  angle pdb=" N   PRO A 435 "
        pdb=" CA  PRO A 435 "
        pdb=" C   PRO A 435 "
      ideal   model   delta    sigma   weight residual
     110.70  114.24   -3.54 1.22e+00 6.72e-01 8.42e+00
  angle pdb=" CA  PRO A 435 "
        pdb=" C   PRO A 435 "
        pdb=" N   PRO A 436 "
      ideal   model   delta    sigma   weight residual
     117.93  121.25   -3.32 1.20e+00 6.94e-01 7.67e+00
  angle pdb=" CA  LEU A 170 "
        pdb=" CB  LEU A 170 "
        pdb=" CG  LEU A 170 "
      ideal   model   delta    sigma   weight residual
     116.30  125.89   -9.59 3.50e+00 8.16e-02 7.51e+00
  angle pdb=" CA  PRO A 458 "
        pdb=" C   PRO A 458 "
        pdb=" N   PRO A 459 "
      ideal   model   delta    sigma   weight residual
     117.93  121.17   -3.24 1.20e+00 6.94e-01 7.28e+00
  ... (remaining 3918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 1488
       17.92 -    35.85: 134
       35.85 -    53.77: 28
       53.77 -    71.70: 1
       71.70 -    89.62: 2
  Dihedral angle restraints: 1653
    sinusoidal: 612
      harmonic: 1041
  Sorted by residual:
  dihedral pdb=" CA  PHE A 346 "
           pdb=" C   PHE A 346 "
           pdb=" N   GLY A 347 "
           pdb=" CA  GLY A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.48   18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  PRO A 458 "
           pdb=" C   PRO A 458 "
           pdb=" N   PRO A 459 "
           pdb=" CA  PRO A 459 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.35   16.65     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  MET A 124 "
           pdb=" CG  MET A 124 "
           pdb=" SD  MET A 124 "
           pdb=" CE  MET A 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  111.65  -51.65     3      1.50e+01 4.44e-03 9.04e+00
  ... (remaining 1650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 236
       0.027 -    0.054: 121
       0.054 -    0.081: 65
       0.081 -    0.108: 26
       0.108 -    0.134: 12
  Chirality restraints: 460
  Sorted by residual:
  chirality pdb=" CG  LEU A 390 "
            pdb=" CB  LEU A 390 "
            pdb=" CD1 LEU A 390 "
            pdb=" CD2 LEU A 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  LEU A 217 "
            pdb=" N   LEU A 217 "
            pdb=" C   LEU A 217 "
            pdb=" CB  LEU A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  PRO A 218 "
            pdb=" N   PRO A 218 "
            pdb=" C   PRO A 218 "
            pdb=" CB  PRO A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.33e-01
  ... (remaining 457 not shown)

  Planarity restraints: 475
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 458 "    0.037 5.00e-02 4.00e+02   5.59e-02 4.99e+00
        pdb=" N   PRO A 459 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 459 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 459 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 434 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.55e+00
        pdb=" N   PRO A 435 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 435 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 435 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 283 "    0.010 2.00e-02 2.50e+03   1.37e-02 3.28e+00
        pdb=" CG  PHE A 283 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 283 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 283 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 283 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 283 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 283 "    0.000 2.00e-02 2.50e+03
  ... (remaining 472 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 794
        2.81 -     3.33: 2950
        3.33 -     3.85: 4865
        3.85 -     4.38: 5349
        4.38 -     4.90: 9133
  Nonbonded interactions: 23091
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 229 "
            pdb=" OG1 THR A 233 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OH  TYR A 293 "
            pdb=" O   ALA A 419 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   TYR A 184 "
            pdb=" OG  SER A 187 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" NH1 ARG A 142 "
            pdb=" O   GLY A 248 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" O   GLN A 362 "
            pdb=" OG  SER A 365 "
     model   vdw
     2.408 3.040
  ... (remaining 23086 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:             0.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.810
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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   0.044   2892  Z= 0.152
  Angle     :  0.722   9.595   3923  Z= 0.361
  Chirality :  0.046   0.134    460
  Planarity :  0.006   0.056    475
  Dihedral  : 14.160  89.622    991
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -0.94 (0.44), residues: 365
  helix: -0.24 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.90 (0.82), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 296 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.031   0.001   PHE A 283 
 TYR   0.006   0.001   TYR A 352 
 ARG   0.001   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13948 (  208)
  hydrogen bonds       : angle       6.86133 (  615)
  covalent geometry    : bond        0.00343 ( 2892)
  covalent geometry    : angle       0.72192 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8002 (tpp) cc_final: 0.7660 (mmt)
REVERT: A   88 GLN cc_start: 0.8661 (mm110) cc_final: 0.8347 (mm-40)
REVERT: A  122 MET cc_start: 0.8886 (tpp) cc_final: 0.8355 (tpp)
REVERT: A  125 ILE cc_start: 0.8579 (mt) cc_final: 0.8306 (mt)
REVERT: A  127 PHE cc_start: 0.8850 (t80) cc_final: 0.8525 (t80)
REVERT: A  185 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8064 (tm-30)
REVERT: A  216 LEU cc_start: 0.9073 (mt) cc_final: 0.8790 (mt)
REVERT: A  246 LEU cc_start: 0.8880 (mt) cc_final: 0.8672 (mt)
REVERT: A  320 GLU cc_start: 0.8892 (pt0) cc_final: 0.8564 (pt0)
REVERT: A  389 CYS cc_start: 0.8771 (m) cc_final: 0.8484 (m)
REVERT: A  391 ILE cc_start: 0.9375 (mp) cc_final: 0.9090 (mp)
REVERT: A  403 MET cc_start: 0.8474 (mmm) cc_final: 0.8272 (tpp)
REVERT: A  448 TYR cc_start: 0.9052 (m-80) cc_final: 0.8654 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1190
  time to fit residues: 19.9445
Evaluate side-chains
  121 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.135254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.125139 restraints weight = 6258.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.128121 restraints weight = 3121.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.130036 restraints weight = 1824.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2892  Z= 0.159
  Angle     :  0.723  10.826   3923  Z= 0.365
  Chirality :  0.046   0.188    460
  Planarity :  0.006   0.051    475
  Dihedral  :  4.108  17.040    387
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 11.51 %
    Favored  : 84.21 %
  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: -0.39 (0.43), residues: 365
  helix:  0.15 (0.29), residues: 311
  sheet:  None (None), residues: 0
  loop : -2.04 (0.80), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.023   0.001   PHE A 285 
 TYR   0.019   0.002   TYR A 172 
 ARG   0.001   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04446 (  208)
  hydrogen bonds       : angle       5.31090 (  615)
  covalent geometry    : bond        0.00360 ( 2892)
  covalent geometry    : angle       0.72326 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7902 (tpp) cc_final: 0.7633 (mmt)
REVERT: A   81 ASN cc_start: 0.8754 (t0) cc_final: 0.8543 (t0)
REVERT: A  122 MET cc_start: 0.9005 (tpp) cc_final: 0.8497 (tpp)
REVERT: A  127 PHE cc_start: 0.8901 (t80) cc_final: 0.8645 (t80)
REVERT: A  185 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: A  216 LEU cc_start: 0.9089 (mt) cc_final: 0.8804 (mt)
REVERT: A  320 GLU cc_start: 0.8784 (pt0) cc_final: 0.8562 (pt0)
REVERT: A  389 CYS cc_start: 0.8706 (m) cc_final: 0.8483 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1155
  time to fit residues: 18.7757
Evaluate side-chains
  127 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  391 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0470
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.136734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.126187 restraints weight = 6230.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.129194 restraints weight = 2954.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.131104 restraints weight = 1672.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   2892  Z= 0.159
  Angle     :  0.737  10.440   3923  Z= 0.373
  Chirality :  0.046   0.148    460
  Planarity :  0.006   0.054    475
  Dihedral  :  4.136  19.178    387
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 21.71 %
    Favored  : 74.67 %
  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: -0.14 (0.45), residues: 365
  helix:  0.32 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -1.86 (0.85), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.019   0.001   PHE A 346 
 TYR   0.022   0.002   TYR A 307 
 ARG   0.002   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04370 (  208)
  hydrogen bonds       : angle       5.23782 (  615)
  covalent geometry    : bond        0.00375 ( 2892)
  covalent geometry    : angle       0.73717 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7958 (tpp) cc_final: 0.7669 (mmt)
REVERT: A   78 MET cc_start: 0.8330 (tmm) cc_final: 0.8103 (tmm)
REVERT: A   81 ASN cc_start: 0.8770 (t0) cc_final: 0.8456 (t0)
REVERT: A  108 ASP cc_start: 0.7882 (p0) cc_final: 0.6886 (p0)
REVERT: A  109 LYS cc_start: 0.8405 (mttt) cc_final: 0.8029 (ttmt)
REVERT: A  122 MET cc_start: 0.9018 (tpp) cc_final: 0.8445 (tpp)
REVERT: A  185 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: A  216 LEU cc_start: 0.9101 (mt) cc_final: 0.8814 (mt)
REVERT: A  320 GLU cc_start: 0.8761 (pt0) cc_final: 0.8525 (pt0)
REVERT: A  372 MET cc_start: 0.8043 (tpp) cc_final: 0.7526 (tpp)
REVERT: A  375 MET cc_start: 0.8420 (mmm) cc_final: 0.7958 (mpp)
REVERT: A  389 CYS cc_start: 0.8715 (m) cc_final: 0.8440 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 125
  average time/residue: 0.1081
  time to fit residues: 16.8608
Evaluate side-chains
  121 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0270
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.136547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.125715 restraints weight = 6315.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.128726 restraints weight = 2977.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.130642 restraints weight = 1695.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   2892  Z= 0.158
  Angle     :  0.729   9.523   3923  Z= 0.370
  Chirality :  0.046   0.159    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.220  19.207    387
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 26.97 %
    Favored  : 69.41 %
  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: -0.30 (0.44), residues: 365
  helix:  0.25 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.18 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.029   0.001   PHE A 285 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.002   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  208)
  hydrogen bonds       : angle       5.24956 (  615)
  covalent geometry    : bond        0.00382 ( 2892)
  covalent geometry    : angle       0.72894 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7931 (tpp) cc_final: 0.7651 (mmt)
REVERT: A   81 ASN cc_start: 0.8791 (t0) cc_final: 0.8393 (t0)
REVERT: A  109 LYS cc_start: 0.8350 (mttt) cc_final: 0.7951 (mmtt)
REVERT: A  122 MET cc_start: 0.9025 (tpp) cc_final: 0.8488 (tpp)
REVERT: A  185 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: A  216 LEU cc_start: 0.9116 (mt) cc_final: 0.8820 (mt)
REVERT: A  320 GLU cc_start: 0.8707 (pt0) cc_final: 0.8491 (pt0)
REVERT: A  375 MET cc_start: 0.8387 (mmm) cc_final: 0.8052 (mpp)
REVERT: A  389 CYS cc_start: 0.8526 (m) cc_final: 0.8319 (m)
  outliers start: 11
  outliers final: 6
  residues processed: 123
  average time/residue: 0.1089
  time to fit residues: 16.9097
Evaluate side-chains
  116 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 313 HIS ** 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 = 0.3901 r_free = 0.3901 target = 0.138317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.127257 restraints weight = 6504.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.130431 restraints weight = 3219.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.132448 restraints weight = 1876.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   2892  Z= 0.165
  Angle     :  0.758   8.432   3923  Z= 0.383
  Chirality :  0.047   0.175    460
  Planarity :  0.006   0.056    475
  Dihedral  :  4.306  21.553    387
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 29.28 %
    Favored  : 66.45 %
  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: -0.13 (0.45), residues: 365
  helix:  0.32 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -1.76 (0.84), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  71 
 HIS   0.001   0.001   HIS A 313 
 PHE   0.019   0.001   PHE A 346 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.002   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (  208)
  hydrogen bonds       : angle       5.34158 (  615)
  covalent geometry    : bond        0.00405 ( 2892)
  covalent geometry    : angle       0.75834 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7999 (tpp) cc_final: 0.7698 (mmt)
REVERT: A   81 ASN cc_start: 0.8714 (t0) cc_final: 0.8305 (t0)
REVERT: A  109 LYS cc_start: 0.8374 (mttt) cc_final: 0.7941 (ttpt)
REVERT: A  122 MET cc_start: 0.9021 (tpp) cc_final: 0.8455 (tpp)
REVERT: A  185 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: A  216 LEU cc_start: 0.9126 (mt) cc_final: 0.8822 (mt)
REVERT: A  320 GLU cc_start: 0.8728 (pt0) cc_final: 0.8521 (pt0)
REVERT: A  375 MET cc_start: 0.8449 (mmm) cc_final: 0.8098 (mpp)
REVERT: A  403 MET cc_start: 0.8631 (tpp) cc_final: 0.8358 (mmm)
  outliers start: 13
  outliers final: 9
  residues processed: 120
  average time/residue: 0.1081
  time to fit residues: 16.1908
Evaluate side-chains
  118 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   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 313 HIS ** 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 = 0.3834 r_free = 0.3834 target = 0.131133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.119986 restraints weight = 6479.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.123196 restraints weight = 3233.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.125227 restraints weight = 1894.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   2892  Z= 0.164
  Angle     :  0.752   7.575   3923  Z= 0.382
  Chirality :  0.047   0.173    460
  Planarity :  0.006   0.056    475
  Dihedral  :  4.272  21.166    387
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 29.93 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.44), residues: 365
  helix:  0.33 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -2.16 (0.79), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  71 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.023   0.001   PHE A 285 
 TYR   0.020   0.002   TYR A 307 
 ARG   0.003   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04034 (  208)
  hydrogen bonds       : angle       5.36286 (  615)
  covalent geometry    : bond        0.00402 ( 2892)
  covalent geometry    : angle       0.75157 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8051 (tpp) cc_final: 0.7711 (mmt)
REVERT: A   81 ASN cc_start: 0.8661 (t0) cc_final: 0.8256 (t0)
REVERT: A  109 LYS cc_start: 0.8404 (mttt) cc_final: 0.8065 (ttpt)
REVERT: A  122 MET cc_start: 0.9037 (tpp) cc_final: 0.8462 (tpp)
REVERT: A  185 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: A  216 LEU cc_start: 0.9122 (mt) cc_final: 0.8820 (mt)
REVERT: A  320 GLU cc_start: 0.8781 (pt0) cc_final: 0.8524 (pt0)
REVERT: A  375 MET cc_start: 0.8408 (mmm) cc_final: 0.8097 (mpp)
REVERT: A  391 ILE cc_start: 0.9447 (mp) cc_final: 0.9141 (mp)
REVERT: A  403 MET cc_start: 0.8629 (tpp) cc_final: 0.8391 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 117
  average time/residue: 0.1147
  time to fit residues: 16.5686
Evaluate side-chains
  121 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 29 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.131248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.120185 restraints weight = 6481.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.123371 restraints weight = 3213.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.125388 restraints weight = 1887.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   2892  Z= 0.160
  Angle     :  0.771   8.150   3923  Z= 0.388
  Chirality :  0.048   0.283    460
  Planarity :  0.006   0.056    475
  Dihedral  :  4.239  20.668    387
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 29.93 %
    Favored  : 64.80 %
  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: -0.10 (0.45), residues: 365
  helix:  0.38 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -2.21 (0.78), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  71 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.022   0.001   PHE A 285 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.002   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  208)
  hydrogen bonds       : angle       5.31086 (  615)
  covalent geometry    : bond        0.00392 ( 2892)
  covalent geometry    : angle       0.77058 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8022 (tpp) cc_final: 0.7652 (mmt)
REVERT: A   79 TRP cc_start: 0.8737 (t-100) cc_final: 0.8444 (t-100)
REVERT: A   81 ASN cc_start: 0.8634 (t0) cc_final: 0.8225 (t0)
REVERT: A  109 LYS cc_start: 0.8217 (mttt) cc_final: 0.7792 (ttpt)
REVERT: A  185 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: A  215 ILE cc_start: 0.9202 (mp) cc_final: 0.8959 (mp)
REVERT: A  216 LEU cc_start: 0.9142 (mt) cc_final: 0.8840 (mt)
REVERT: A  320 GLU cc_start: 0.8767 (pt0) cc_final: 0.8477 (pt0)
REVERT: A  333 MET cc_start: 0.8865 (mmp) cc_final: 0.8619 (mmp)
REVERT: A  375 MET cc_start: 0.8398 (mmm) cc_final: 0.8099 (mpp)
REVERT: A  403 MET cc_start: 0.8552 (tpp) cc_final: 0.8331 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1126
  time to fit residues: 16.9406
Evaluate side-chains
  123 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 TYR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0170
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** A 313 HIS ** 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 = 0.3861 r_free = 0.3861 target = 0.133634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.123195 restraints weight = 6433.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.126237 restraints weight = 3206.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.128163 restraints weight = 1875.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   2892  Z= 0.159
  Angle     :  0.776   7.667   3923  Z= 0.394
  Chirality :  0.047   0.183    460
  Planarity :  0.006   0.056    475
  Dihedral  :  4.257  20.497    387
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 31.91 %
    Favored  : 63.82 %
  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: -0.12 (0.45), residues: 365
  helix:  0.39 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.27 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A  71 
 HIS   0.002   0.001   HIS A 317 
 PHE   0.035   0.001   PHE A 127 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.002   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  208)
  hydrogen bonds       : angle       5.38430 (  615)
  covalent geometry    : bond        0.00386 ( 2892)
  covalent geometry    : angle       0.77631 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7970 (tpp) cc_final: 0.7612 (mmt)
REVERT: A   79 TRP cc_start: 0.8738 (t-100) cc_final: 0.8441 (t-100)
REVERT: A   81 ASN cc_start: 0.8675 (t0) cc_final: 0.8245 (t0)
REVERT: A  109 LYS cc_start: 0.8259 (mttt) cc_final: 0.7845 (mmtt)
REVERT: A  185 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7628 (tm-30)
REVERT: A  215 ILE cc_start: 0.9228 (mp) cc_final: 0.8980 (mp)
REVERT: A  216 LEU cc_start: 0.9122 (mt) cc_final: 0.8825 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1195
  time to fit residues: 17.3876
Evaluate side-chains
  125 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ARG
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 TYR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   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 313 HIS ** 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 = 0.3910 r_free = 0.3910 target = 0.138203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.126990 restraints weight = 6458.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.130164 restraints weight = 3211.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.132258 restraints weight = 1881.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   2892  Z= 0.164
  Angle     :  0.814   8.195   3923  Z= 0.405
  Chirality :  0.047   0.185    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.265  20.379    387
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 32.57 %
    Favored  : 62.83 %
  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: -0.14 (0.45), residues: 365
  helix:  0.39 (0.30), residues: 309
  sheet:  None (None), residues: 0
  loop : -2.34 (0.77), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A  71 
 HIS   0.004   0.002   HIS A 313 
 PHE   0.033   0.001   PHE A 127 
 TYR   0.018   0.002   TYR A 307 
 ARG   0.001   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  208)
  hydrogen bonds       : angle       5.39835 (  615)
  covalent geometry    : bond        0.00400 ( 2892)
  covalent geometry    : angle       0.81387 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7942 (tpp) cc_final: 0.7562 (mmt)
REVERT: A   79 TRP cc_start: 0.8746 (t-100) cc_final: 0.8408 (t-100)
REVERT: A   81 ASN cc_start: 0.8708 (t0) cc_final: 0.8277 (t0)
REVERT: A  109 LYS cc_start: 0.8301 (mttt) cc_final: 0.7845 (mmtt)
REVERT: A  185 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: A  216 LEU cc_start: 0.9122 (mt) cc_final: 0.8817 (mt)
REVERT: A  375 MET cc_start: 0.8384 (mmm) cc_final: 0.7922 (mpp)
  outliers start: 14
  outliers final: 11
  residues processed: 127
  average time/residue: 0.1120
  time to fit residues: 17.7500
Evaluate side-chains
  124 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 ARG
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 TYR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.138345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.126583 restraints weight = 6577.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.129780 restraints weight = 3329.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.131857 restraints weight = 1966.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   2892  Z= 0.173
  Angle     :  0.857   9.126   3923  Z= 0.430
  Chirality :  0.048   0.188    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.317  20.941    387
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 33.22 %
    Favored  : 62.50 %
  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: -0.23 (0.45), residues: 365
  helix:  0.32 (0.30), residues: 309
  sheet:  None (None), residues: 0
  loop : -2.30 (0.78), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.034   0.002   PHE A 127 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.001   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04165 (  208)
  hydrogen bonds       : angle       5.48905 (  615)
  covalent geometry    : bond        0.00432 ( 2892)
  covalent geometry    : angle       0.85698 ( 3923)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7890 (tpp) cc_final: 0.7523 (mmt)
REVERT: A   79 TRP cc_start: 0.8757 (t-100) cc_final: 0.8447 (t-100)
REVERT: A   81 ASN cc_start: 0.8719 (t0) cc_final: 0.8273 (t0)
REVERT: A  109 LYS cc_start: 0.8235 (mttt) cc_final: 0.7804 (mmtt)
REVERT: A  185 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7523 (tm-30)
REVERT: A  216 LEU cc_start: 0.9134 (mt) cc_final: 0.8862 (mt)
REVERT: A  375 MET cc_start: 0.8363 (mmm) cc_final: 0.7933 (mpp)
  outliers start: 13
  outliers final: 13
  residues processed: 122
  average time/residue: 0.1135
  time to fit residues: 17.3309
Evaluate side-chains
  129 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 ARG
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 TYR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  422 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.136688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.124831 restraints weight = 6386.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.127941 restraints weight = 3142.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.129959 restraints weight = 1811.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   2892  Z= 0.175
  Angle     :  0.855   9.597   3923  Z= 0.432
  Chirality :  0.049   0.184    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.277  20.883    387
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 18.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 34.21 %
    Favored  : 61.51 %
  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: -0.25 (0.45), residues: 365
  helix:  0.30 (0.30), residues: 309
  sheet:  None (None), residues: 0
  loop : -2.27 (0.78), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.034   0.002   PHE A 127 
 TYR   0.017   0.002   TYR A 307 
 ARG   0.001   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04181 (  208)
  hydrogen bonds       : angle       5.52028 (  615)
  covalent geometry    : bond        0.00441 ( 2892)
  covalent geometry    : angle       0.85491 ( 3923)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1218.75 seconds
wall clock time: 22 minutes 21.01 seconds (1341.01 seconds total)