Starting phenix.real_space_refine
on Wed Sep 17 03:17:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hhq_52173/09_2025/9hhq_52173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hhq_52173/09_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_52173/09_2025/9hhq_52173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hhq_52173/09_2025/9hhq_52173.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hhq_52173/09_2025/9hhq_52173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hhq_52173/09_2025/9hhq_52173.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.03, per 1000 atoms: 0.37
  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: 0.16
  Conformation dependent library (CDL) restraints added in 125.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.09
  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: 0.44

  Time building geometry restraints manager: 0.23 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:             0.310
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.710
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.140
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG A 235 
 TYR   0.006   0.001   TYR A 352 
 PHE   0.031   0.001   PHE A 283 
 TRP   0.004   0.001   TRP A 296 
 HIS   0.002   0.001   HIS A 313 

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

*********************** 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  : 0.063 
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: 0.0447
  time to fit residues: 7.6075
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  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0670
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0060
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.4934

-------------------------------------------------------------------------------
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 = 0.3906 r_free = 0.3906 target = 0.136491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.126238 restraints weight = 6272.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.128994 restraints weight = 3139.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.131069 restraints weight = 1915.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.132427 restraints weight = 1222.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.133360 restraints weight = 829.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   2892  Z= 0.160
  Angle     :  0.718  10.586   3923  Z= 0.361
  Chirality :  0.045   0.165    460
  Planarity :  0.006   0.051    475
  Dihedral  :  4.092  17.266    387
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 11.18 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.44), residues: 365
  helix:  0.16 (0.29), residues: 309
  sheet:  None (None), residues: 0
  loop : -1.60 (0.86), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 321 
 TYR   0.018   0.002   TYR A 172 
 PHE   0.022   0.001   PHE A 285 
 TRP   0.014   0.002   TRP A  71 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2892)
  covalent geometry    : angle       0.71780 ( 3923)
  hydrogen bonds       : bond        0.04592 (  208)
  hydrogen bonds       : angle       5.34292 (  615)

*********************** 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: 12
    poor density    : 128
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8825 (t0) cc_final: 0.8622 (t0)
REVERT: A  122 MET cc_start: 0.8992 (tpp) cc_final: 0.8465 (tpp)
REVERT: A  127 PHE cc_start: 0.8877 (t80) cc_final: 0.8637 (t80)
REVERT: A  185 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: A  216 LEU cc_start: 0.9071 (mt) cc_final: 0.8787 (mt)
REVERT: A  320 GLU cc_start: 0.8742 (pt0) cc_final: 0.8523 (pt0)
REVERT: A  389 CYS cc_start: 0.8619 (m) cc_final: 0.8407 (m)
  outliers start: 12
  outliers final: 9
  residues processed: 133
  average time/residue: 0.0439
  time to fit residues: 7.3425
Evaluate side-chains
  124 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
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  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 10 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.131977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.121964 restraints weight = 6332.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.125008 restraints weight = 2985.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.126942 restraints weight = 1693.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.128278 restraints weight = 1056.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.129202 restraints weight = 703.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   2892  Z= 0.161
  Angle     :  0.732  10.184   3923  Z= 0.370
  Chirality :  0.045   0.152    460
  Planarity :  0.006   0.054    475
  Dihedral  :  4.115  19.035    387
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 22.04 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.45), residues: 365
  helix:  0.32 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -1.90 (0.84), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 321 
 TYR   0.022   0.002   TYR A 307 
 PHE   0.025   0.001   PHE A 285 
 TRP   0.018   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 2892)
  covalent geometry    : angle       0.73221 ( 3923)
  hydrogen bonds       : bond        0.04382 (  208)
  hydrogen bonds       : angle       5.26222 (  615)

*********************** 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
  135 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.8305 (tmm) cc_final: 0.8084 (tmm)
REVERT: A   81 ASN cc_start: 0.8757 (t0) cc_final: 0.8450 (t0)
REVERT: A  108 ASP cc_start: 0.7854 (p0) cc_final: 0.6919 (p0)
REVERT: A  109 LYS cc_start: 0.8418 (mttt) cc_final: 0.8044 (ttmt)
REVERT: A  122 MET cc_start: 0.8985 (tpp) cc_final: 0.8416 (tpp)
REVERT: A  185 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7647 (tm-30)
REVERT: A  216 LEU cc_start: 0.9093 (mt) cc_final: 0.8805 (mt)
REVERT: A  320 GLU cc_start: 0.8743 (pt0) cc_final: 0.8487 (pt0)
REVERT: A  372 MET cc_start: 0.8040 (tpp) cc_final: 0.7488 (tpp)
REVERT: A  375 MET cc_start: 0.8421 (mmm) cc_final: 0.7969 (mpp)
REVERT: A  389 CYS cc_start: 0.8684 (m) cc_final: 0.8398 (m)
  outliers start: 15
  outliers final: 12
  residues processed: 126
  average time/residue: 0.0400
  time to fit residues: 6.4544
Evaluate side-chains
  126 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue  124 MET
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  178 CYS
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  391 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN
A 418 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.137645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.126752 restraints weight = 6318.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.129771 restraints weight = 3002.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.131823 restraints weight = 1725.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.133170 restraints weight = 1072.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.134105 restraints weight = 715.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   2892  Z= 0.154
  Angle     :  0.730   8.598   3923  Z= 0.368
  Chirality :  0.046   0.159    460
  Planarity :  0.006   0.056    475
  Dihedral  :  4.130  19.276    387
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 26.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.44), residues: 365
  helix:  0.27 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.24 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 321 
 TYR   0.019   0.002   TYR A 307 
 PHE   0.017   0.001   PHE A 285 
 TRP   0.021   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2892)
  covalent geometry    : angle       0.72951 ( 3923)
  hydrogen bonds       : bond        0.04170 (  208)
  hydrogen bonds       : angle       5.25145 (  615)

*********************** 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
  131 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.063 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8759 (t0) cc_final: 0.8358 (t0)
REVERT: A  109 LYS cc_start: 0.8285 (mttt) cc_final: 0.7922 (mmtt)
REVERT: A  122 MET cc_start: 0.8998 (tpp) cc_final: 0.8433 (tpp)
REVERT: A  185 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7579 (tm-30)
REVERT: A  216 LEU cc_start: 0.9095 (mt) cc_final: 0.8798 (mt)
REVERT: A  320 GLU cc_start: 0.8695 (pt0) cc_final: 0.8462 (pt0)
REVERT: A  375 MET cc_start: 0.8407 (mmm) cc_final: 0.8071 (mpp)
  outliers start: 12
  outliers final: 8
  residues processed: 123
  average time/residue: 0.0475
  time to fit residues: 7.3707
Evaluate side-chains
  117 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 MET
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  353 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0370
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0010
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4864

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.138995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.127733 restraints weight = 6320.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.130947 restraints weight = 3108.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.132896 restraints weight = 1765.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.134217 restraints weight = 1107.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.135137 restraints weight = 737.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3456

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= 0.159
  Angle     :  0.745   7.901   3923  Z= 0.379
  Chirality :  0.046   0.169    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.224  21.615    387
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 29.61 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.44), residues: 365
  helix:  0.27 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.20 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 321 
 TYR   0.019   0.002   TYR A 307 
 PHE   0.032   0.001   PHE A 285 
 TRP   0.022   0.002   TRP A  71 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 2892)
  covalent geometry    : angle       0.74457 ( 3923)
  hydrogen bonds       : bond        0.04141 (  208)
  hydrogen bonds       : angle       5.28145 (  615)

*********************** 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  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8768 (t0) cc_final: 0.8344 (t0)
REVERT: A  108 ASP cc_start: 0.7727 (p0) cc_final: 0.7484 (p0)
REVERT: A  109 LYS cc_start: 0.8245 (mttt) cc_final: 0.7882 (ttpt)
REVERT: A  185 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7639 (tm-30)
REVERT: A  216 LEU cc_start: 0.9103 (mt) cc_final: 0.8802 (mt)
REVERT: A  375 MET cc_start: 0.8400 (mmm) cc_final: 0.8144 (mpp)
REVERT: A  403 MET cc_start: 0.8573 (tpp) cc_final: 0.8336 (mmm)
  outliers start: 13
  outliers final: 11
  residues processed: 122
  average time/residue: 0.0449
  time to fit residues: 6.8993
Evaluate side-chains
  122 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  124 MET
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  291 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  366 PHE
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 35 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.134940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.124055 restraints weight = 6371.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.127065 restraints weight = 3133.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.129026 restraints weight = 1829.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.130351 restraints weight = 1148.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.131306 restraints weight = 772.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2892  Z= 0.159
  Angle     :  0.752   7.496   3923  Z= 0.383
  Chirality :  0.047   0.172    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.204  20.838    387
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 29.28 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.45), residues: 365
  helix:  0.31 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.15 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 222 
 TYR   0.020   0.002   TYR A 307 
 PHE   0.024   0.001   PHE A 285 
 TRP   0.025   0.002   TRP A  71 
 HIS   0.004   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 2892)
  covalent geometry    : angle       0.75157 ( 3923)
  hydrogen bonds       : bond        0.04025 (  208)
  hydrogen bonds       : angle       5.30249 (  615)

*********************** 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: 14
    poor density    : 112
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8759 (t0) cc_final: 0.8326 (t0)
REVERT: A  109 LYS cc_start: 0.8289 (mttt) cc_final: 0.7904 (ttpt)
REVERT: A  185 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: A  216 LEU cc_start: 0.9111 (mt) cc_final: 0.8822 (mt)
REVERT: A  375 MET cc_start: 0.8306 (mmm) cc_final: 0.8102 (mpp)
REVERT: A  391 ILE cc_start: 0.9436 (mp) cc_final: 0.9143 (mp)
REVERT: A  448 TYR cc_start: 0.8931 (m-80) cc_final: 0.8507 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0456
  time to fit residues: 6.7483
Evaluate side-chains
  118 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  124 MET
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  361 LEU
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0050
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6594

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.134248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.122803 restraints weight = 6313.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.125737 restraints weight = 3092.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.127731 restraints weight = 1819.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.129085 restraints weight = 1147.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.130047 restraints weight = 770.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3730

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= 0.159
  Angle     :  0.766   7.754   3923  Z= 0.387
  Chirality :  0.048   0.269    460
  Planarity :  0.006   0.056    475
  Dihedral  :  4.130  20.091    387
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 32.57 %
    Favored  : 63.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.45), residues: 365
  helix:  0.38 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -2.18 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 321 
 TYR   0.019   0.002   TYR A 307 
 PHE   0.021   0.001   PHE A 285 
 TRP   0.027   0.002   TRP A  71 
 HIS   0.004   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 2892)
  covalent geometry    : angle       0.76589 ( 3923)
  hydrogen bonds       : bond        0.04026 (  208)
  hydrogen bonds       : angle       5.26300 (  615)

*********************** 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
  126 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8740 (t0) cc_final: 0.8327 (t0)
REVERT: A  109 LYS cc_start: 0.8133 (mttt) cc_final: 0.7752 (ttpt)
REVERT: A  122 MET cc_start: 0.9089 (tpt) cc_final: 0.8810 (tpp)
REVERT: A  185 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: A  216 LEU cc_start: 0.9099 (mt) cc_final: 0.8814 (mt)
REVERT: A  375 MET cc_start: 0.8286 (mmm) cc_final: 0.8082 (mpp)
REVERT: A  448 TYR cc_start: 0.8920 (m-80) cc_final: 0.8524 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 118
  average time/residue: 0.0475
  time to fit residues: 7.0604
Evaluate side-chains
  116 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 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  366 PHE
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 4 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.135211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.124064 restraints weight = 6369.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.127164 restraints weight = 3132.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.129115 restraints weight = 1809.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.130485 restraints weight = 1144.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.131340 restraints weight = 775.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3862

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= 0.160
  Angle     :  0.779   7.805   3923  Z= 0.395
  Chirality :  0.047   0.176    460
  Planarity :  0.006   0.056    475
  Dihedral  :  4.126  20.241    387
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 32.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.45), residues: 365
  helix:  0.33 (0.30), residues: 309
  sheet:  None (None), residues: 0
  loop : -2.32 (0.79), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 321 
 TYR   0.019   0.002   TYR A 307 
 PHE   0.032   0.001   PHE A 242 
 TRP   0.030   0.002   TRP A  71 
 HIS   0.004   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 2892)
  covalent geometry    : angle       0.77923 ( 3923)
  hydrogen bonds       : bond        0.04043 (  208)
  hydrogen bonds       : angle       5.34601 (  615)

*********************** 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
  128 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8707 (t0) cc_final: 0.8305 (t0)
REVERT: A  109 LYS cc_start: 0.8196 (mttt) cc_final: 0.7818 (mmtt)
REVERT: A  122 MET cc_start: 0.9092 (tpt) cc_final: 0.8793 (tpp)
REVERT: A  185 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7604 (tm-30)
REVERT: A  216 LEU cc_start: 0.9102 (mt) cc_final: 0.8814 (mt)
REVERT: A  448 TYR cc_start: 0.8921 (m-80) cc_final: 0.8480 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 120
  average time/residue: 0.0466
  time to fit residues: 7.1066
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  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  201 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  366 PHE
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  371 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 27 optimal weight:    5.9990
   chunk 3 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0670
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.134366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.124108 restraints weight = 6372.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.127066 restraints weight = 3147.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.128945 restraints weight = 1845.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.130360 restraints weight = 1181.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.131272 restraints weight = 803.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   2892  Z= 0.163
  Angle     :  0.819   8.535   3923  Z= 0.412
  Chirality :  0.048   0.173    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.142  20.549    387
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 33.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.45), residues: 365
  helix:  0.33 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.44 (0.77), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 321 
 TYR   0.020   0.002   TYR A 307 
 PHE   0.027   0.001   PHE A 242 
 TRP   0.032   0.002   TRP A  71 
 HIS   0.004   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 2892)
  covalent geometry    : angle       0.81865 ( 3923)
  hydrogen bonds       : bond        0.04084 (  208)
  hydrogen bonds       : angle       5.43595 (  615)

*********************** 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
  125 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8753 (t0) cc_final: 0.8352 (t0)
REVERT: A  109 LYS cc_start: 0.8200 (mttt) cc_final: 0.7798 (mmtt)
REVERT: A  122 MET cc_start: 0.9081 (tpt) cc_final: 0.8777 (tpp)
REVERT: A  185 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: A  216 LEU cc_start: 0.9085 (mt) cc_final: 0.8805 (mt)
REVERT: A  448 TYR cc_start: 0.8906 (m-80) cc_final: 0.8479 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 118
  average time/residue: 0.0460
  time to fit residues: 6.9203
Evaluate side-chains
  120 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
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  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  366 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 11 optimal weight:    0.1980
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.139856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.128176 restraints weight = 6477.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.131415 restraints weight = 3212.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.133510 restraints weight = 1851.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.134940 restraints weight = 1168.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.135897 restraints weight = 780.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   2892  Z= 0.174
  Angle     :  0.879  12.184   3923  Z= 0.437
  Chirality :  0.048   0.195    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.149  20.542    387
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 19.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 34.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.45), residues: 365
  helix:  0.28 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.42 (0.77), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 321 
 TYR   0.019   0.002   TYR A 307 
 PHE   0.023   0.001   PHE A 285 
 TRP   0.033   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 2892)
  covalent geometry    : angle       0.87910 ( 3923)
  hydrogen bonds       : bond        0.04268 (  208)
  hydrogen bonds       : angle       5.48089 (  615)

********************** 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
  123 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8749 (t0) cc_final: 0.8273 (t0)
REVERT: A  109 LYS cc_start: 0.8147 (mttt) cc_final: 0.7793 (mmtt)
REVERT: A  185 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7528 (tm-30)
REVERT: A  216 LEU cc_start: 0.9083 (mt) cc_final: 0.8807 (mt)
REVERT: A  368 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8147 (t80)
REVERT: A  448 TYR cc_start: 0.8918 (m-80) cc_final: 0.8488 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 117
  average time/residue: 0.0480
  time to fit residues: 7.1467
Evaluate side-chains
  120 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
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  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  366 PHE
Chi-restraints excluded: chain A residue  368 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.2980
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0020
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.4728

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.142166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.130747 restraints weight = 6277.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.133568 restraints weight = 3095.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.135844 restraints weight = 1867.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.137295 restraints weight = 1166.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.138294 restraints weight = 776.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   2892  Z= 0.169
  Angle     :  0.888  10.541   3923  Z= 0.441
  Chirality :  0.048   0.184    460
  Planarity :  0.006   0.055    475
  Dihedral  :  4.159  20.663    387
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 33.22 %
    Favored  : 63.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.45), residues: 365
  helix:  0.32 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.42 (0.77), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 321 
 TYR   0.019   0.002   TYR A 307 
 PHE   0.046   0.002   PHE A 242 
 TRP   0.033   0.002   TRP A  71 
 HIS   0.004   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 2892)
  covalent geometry    : angle       0.88838 ( 3923)
  hydrogen bonds       : bond        0.04204 (  208)
  hydrogen bonds       : angle       5.54667 (  615)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 651.74 seconds
wall clock time: 11 minutes 54.29 seconds (714.29 seconds total)