Starting phenix.real_space_refine
on Wed Sep 17 03:17:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kqa_62498/09_2025/9kqa_62498.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kqa_62498/09_2025/9kqa_62498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kqa_62498/09_2025/9kqa_62498.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kqa_62498/09_2025/9kqa_62498.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kqa_62498/09_2025/9kqa_62498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kqa_62498/09_2025/9kqa_62498.map"
  }
  resolution = 3.28
  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=   0.075
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      23      5.16       5
     C    1861      2.51       5
     N     428      2.21       5
     O     471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  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: 2783
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2760
          Classifications: {'peptide': 377}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 23, 'TRANS': 353}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'EBZ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.99, per 1000 atoms: 0.36
  Number of scatterers: 2783
  At special positions: 0
  Unit cell: (69.9, 52.192, 63.376, 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      23     16.00
     O     471      8.00
     N     428      7.00
     C    1861      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: 0.29
  Conformation dependent library (CDL) restraints added in 134.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  678

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      86.7% 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 18 through 39
    Processing helix  chain 'A' and resid 40 through 43
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 129 through 157
      removed outlier: 4.328A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
      removed outlier: 3.795A  pdb=" N   ASN A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 178
      removed outlier: 4.161A  pdb=" N   PHE A 170 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A 171 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 211
      removed outlier: 3.747A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 246
      removed outlier: 3.505A  pdb=" N   ARG A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
      Proline residue:  A 236  - end of helix
    Processing helix  chain 'A' and resid 248 through 270
      removed outlier: 4.599A  pdb=" N   PHE A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 291
    Processing helix  chain 'A' and resid 291 through 312
      removed outlier: 3.754A  pdb=" N   LEU A 295 " --> pdb=" O   ASP A 291 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   GLY A 307 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLU A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 352
      removed outlier: 3.795A  pdb=" N   SER A 340 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE A 347 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   ILE A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 375
      removed outlier: 3.541A  pdb=" N   CYS A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 414
      removed outlier: 3.689A  pdb=" N   ASN A 388 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
      removed outlier: 4.144A  pdb=" N   GLY A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 431
    Processing helix  chain 'A' and resid 431 through 436
    Processing helix  chain 'A' and resid 436 through 448
    Processing helix  chain 'A' and resid 448 through 464
      removed outlier: 4.814A  pdb=" N   THR A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 3.577A  pdb=" N   PHE A 469 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    669 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: 0.53

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 831
        1.34 -     1.46: 595
        1.46 -     1.58: 1387
        1.58 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 2852
  Sorted by residual:
  bond pdb=" C12 EBZ A 601 "
       pdb=" N04 EBZ A 601 "
    ideal  model  delta    sigma   weight residual
    1.452  1.545 -0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" C05 EBZ A 601 "
       pdb=" N04 EBZ A 601 "
    ideal  model  delta    sigma   weight residual
    1.460  1.544 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" C11 EBZ A 601 "
       pdb=" N04 EBZ A 601 "
    ideal  model  delta    sigma   weight residual
    1.465  1.548 -0.083 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" CA  ILE A 265 "
       pdb=" C   ILE A 265 "
    ideal  model  delta    sigma   weight residual
    1.524  1.501  0.022 1.22e-02 6.72e+03 3.37e+00
  bond pdb=" CA  ILE A 456 "
       pdb=" C   ILE A 456 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.021 1.22e-02 6.72e+03 2.91e+00
  ... (remaining 2847 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 3756
        1.88 -     3.75: 110
        3.75 -     5.63: 22
        5.63 -     7.50: 4
        7.50 -     9.38: 2
  Bond angle restraints: 3894
  Sorted by residual:
  angle pdb=" C   ILE A 375 "
        pdb=" CA  ILE A 375 "
        pdb=" CB  ILE A 375 "
      ideal   model   delta    sigma   weight residual
     113.70  107.75    5.95 9.50e-01 1.11e+00 3.92e+01
  angle pdb=" N   VAL A 332 "
        pdb=" CA  VAL A 332 "
        pdb=" C   VAL A 332 "
      ideal   model   delta    sigma   weight residual
     111.91  106.86    5.05 8.90e-01 1.26e+00 3.21e+01
  angle pdb=" CA  ILE A 375 "
        pdb=" C   ILE A 375 "
        pdb=" N   PRO A 376 "
      ideal   model   delta    sigma   weight residual
     120.83  117.61    3.22 5.90e-01 2.87e+00 2.97e+01
  angle pdb=" N   LEU A 191 "
        pdb=" CA  LEU A 191 "
        pdb=" C   LEU A 191 "
      ideal   model   delta    sigma   weight residual
     110.97  106.10    4.87 1.09e+00 8.42e-01 1.99e+01
  angle pdb=" C   ILE A 381 "
        pdb=" CA  ILE A 381 "
        pdb=" CB  ILE A 381 "
      ideal   model   delta    sigma   weight residual
     112.02  107.22    4.80 1.31e+00 5.83e-01 1.34e+01
  ... (remaining 3889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.17: 1618
       33.17 -    66.35: 47
       66.35 -    99.52: 8
       99.52 -   132.69: 0
      132.69 -   165.87: 1
  Dihedral angle restraints: 1674
    sinusoidal: 610
      harmonic: 1064
  Sorted by residual:
  dihedral pdb=" C13 EBZ A 601 "
           pdb=" C18 EBZ A 601 "
           pdb=" C19 EBZ A 601 "
           pdb=" C23 EBZ A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.15 -134.98 -165.87     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C10 EBZ A 601 "
           pdb=" C11 EBZ A 601 "
           pdb=" C13 EBZ A 601 "
           pdb=" N04 EBZ A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.85  -39.25   93.10     1      3.00e+01 1.11e-03 1.12e+01
  dihedral pdb=" C18 EBZ A 601 "
           pdb=" C11 EBZ A 601 "
           pdb=" C13 EBZ A 601 "
           pdb=" N04 EBZ A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -69.60 -162.56   92.96     1      3.00e+01 1.11e-03 1.12e+01
  ... (remaining 1671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 287
       0.032 -    0.065: 114
       0.065 -    0.097: 51
       0.097 -    0.129: 15
       0.129 -    0.162: 4
  Chirality restraints: 471
  Sorted by residual:
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  VAL A 368 "
            pdb=" N   VAL A 368 "
            pdb=" C   VAL A 368 "
            pdb=" CB  VAL A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  VAL A 332 "
            pdb=" N   VAL A 332 "
            pdb=" C   VAL A 332 "
            pdb=" CB  VAL A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 468 not shown)

  Planarity restraints: 477
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C05 EBZ A 601 "   -0.364 2.00e-02 2.50e+03   2.39e-01 1.42e+03
        pdb=" C06 EBZ A 601 "   -0.102 2.00e-02 2.50e+03
        pdb=" C07 EBZ A 601 "   -0.100 2.00e-02 2.50e+03
        pdb=" C09 EBZ A 601 "    0.381 2.00e-02 2.50e+03
        pdb=" C14 EBZ A 601 "    0.200 2.00e-02 2.50e+03
        pdb=" C15 EBZ A 601 "    0.287 2.00e-02 2.50e+03
        pdb=" C16 EBZ A 601 "    0.066 2.00e-02 2.50e+03
        pdb=" C17 EBZ A 601 "    0.100 2.00e-02 2.50e+03
        pdb=" O01 EBZ A 601 "   -0.122 2.00e-02 2.50e+03
        pdb=" O02 EBZ A 601 "   -0.346 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 160 "    0.040 5.00e-02 4.00e+02   6.10e-02 5.96e+00
        pdb=" N   PRO A 161 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 161 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 161 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 449 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.16e+00
        pdb=" N   PRO A 450 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 450 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 450 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 474 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 432
        2.75 -     3.29: 2938
        3.29 -     3.82: 4838
        3.82 -     4.36: 5218
        4.36 -     4.90: 9138
  Nonbonded interactions: 22564
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 176 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OD2 ASP A 411 "
            pdb=" OH  TYR A 418 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" ND2 ASN A 146 "
            pdb=" OD2 ASP A 426 "
     model   vdw
     2.406 3.120
  nonbonded pdb=" OH  TYR A  47 "
            pdb=" NZ  LYS A 248 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" O   ASP A 214 "
            pdb=" N   ARG A 217 "
     model   vdw
     2.442 3.120
  ... (remaining 22559 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  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:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.880
  Find NCS groups from input model:        0.010
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
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      :  0.005   0.093   2852  Z= 0.283
  Angle     :  0.791   9.378   3894  Z= 0.476
  Chirality :  0.044   0.162    471
  Planarity :  0.012   0.239    477
  Dihedral  : 17.319 165.867    996
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 23.78 %
    Favored  : 75.87 %
  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: -2.72 (0.39), residues: 371
  helix: -1.17 (0.27), residues: 297
  sheet:  None (None), residues: 0
  loop : -3.86 (0.65), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.013   0.002   PHE A 238 
 TRP   0.010   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 2852)
  covalent geometry    : angle       0.79131 ( 3894)
  hydrogen bonds       : bond        0.12522 (  227)
  hydrogen bonds       : angle       6.38656 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.9039 (m-40) cc_final: 0.8578 (m-40)
REVERT: A  268 PHE cc_start: 0.7354 (t80) cc_final: 0.6786 (t80)
REVERT: A  280 GLN cc_start: 0.8512 (mt0) cc_final: 0.7988 (mt0)
REVERT: A  289 LEU cc_start: 0.8433 (mt) cc_final: 0.8181 (mt)
REVERT: A  328 TRP cc_start: 0.5209 (m100) cc_final: 0.3139 (p90)
REVERT: A  329 GLN cc_start: 0.6983 (mt0) cc_final: 0.6713 (mm-40)
REVERT: A  354 LYS cc_start: 0.8501 (tttt) cc_final: 0.8088 (mtpp)
REVERT: A  463 PHE cc_start: 0.6722 (t80) cc_final: 0.6321 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 89
  average time/residue: 0.0533
  time to fit residues: 5.8865
Evaluate side-chains
  70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0370
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0970
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 154 ASN
A 192 GLN
A 305 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.145137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.130110 restraints weight = 3867.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.87
r_work: 0.3543 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2852  Z= 0.143
  Angle     :  0.655   8.545   3894  Z= 0.319
  Chirality :  0.042   0.140    471
  Planarity :  0.005   0.055    477
  Dihedral  : 11.163 137.395    428
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 32.17 %
    Favored  : 63.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.42 (0.45), residues: 371
  helix:  0.58 (0.31), residues: 294
  sheet:  None (None), residues: 0
  loop : -3.58 (0.65), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.024   0.002   PHE A 348 
 TRP   0.011   0.001   TRP A 318 
 HIS   0.001   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 2852)
  covalent geometry    : angle       0.65537 ( 3894)
  hydrogen bonds       : bond        0.04167 (  227)
  hydrogen bonds       : angle       5.20142 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  268 PHE cc_start: 0.7544 (t80) cc_final: 0.6964 (t80)
REVERT: A  280 GLN cc_start: 0.8452 (mt0) cc_final: 0.7939 (mt0)
REVERT: A  329 GLN cc_start: 0.7321 (mt0) cc_final: 0.6799 (mm-40)
REVERT: A  354 LYS cc_start: 0.8588 (tttt) cc_final: 0.8165 (mtpp)
REVERT: A  463 PHE cc_start: 0.7095 (t80) cc_final: 0.6738 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0391
  time to fit residues: 3.8682
Evaluate side-chains
  66 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  421 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0370
   chunk 11 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.147495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.131764 restraints weight = 3943.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 2.97
r_work: 0.3583 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2852  Z= 0.146
  Angle     :  0.642   6.954   3894  Z= 0.309
  Chirality :  0.043   0.127    471
  Planarity :  0.005   0.053    477
  Dihedral  : 11.079 141.965    428
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 32.87 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.47 (0.46), residues: 371
  helix:  1.17 (0.31), residues: 297
  sheet:  None (None), residues: 0
  loop : -3.28 (0.66), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 357 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.024   0.002   PHE A 348 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 2852)
  covalent geometry    : angle       0.64229 ( 3894)
  hydrogen bonds       : bond        0.03829 (  227)
  hydrogen bonds       : angle       4.98989 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A  268 PHE cc_start: 0.7664 (t80) cc_final: 0.7169 (t80)
REVERT: A  280 GLN cc_start: 0.8574 (mt0) cc_final: 0.8117 (mt0)
REVERT: A  329 GLN cc_start: 0.7519 (mt0) cc_final: 0.6918 (mm110)
REVERT: A  354 LYS cc_start: 0.8626 (tttt) cc_final: 0.8199 (mtpp)
REVERT: A  365 MET cc_start: 0.7855 (mmm) cc_final: 0.7535 (mmm)
REVERT: A  384 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6917 (mp)
REVERT: A  415 VAL cc_start: 0.8506 (t) cc_final: 0.8090 (p)
REVERT: A  463 PHE cc_start: 0.7235 (t80) cc_final: 0.6962 (t80)
  outliers start: 10
  outliers final: 5
  residues processed: 70
  average time/residue: 0.0354
  time to fit residues: 3.3814
Evaluate side-chains
  66 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  405 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0870
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.146924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.131120 restraints weight = 3900.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.95
r_work: 0.3568 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2852  Z= 0.145
  Angle     :  0.624   7.553   3894  Z= 0.299
  Chirality :  0.042   0.120    471
  Planarity :  0.005   0.051    477
  Dihedral  : 11.101 145.070    428
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 32.87 %
    Favored  : 62.59 %
  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:  0.90 (0.46), residues: 371
  helix:  1.48 (0.32), residues: 298
  sheet:  None (None), residues: 0
  loop : -3.22 (0.64), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.021   0.002   PHE A 468 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2852)
  covalent geometry    : angle       0.62367 ( 3894)
  hydrogen bonds       : bond        0.03742 (  227)
  hydrogen bonds       : angle       4.94746 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A  268 PHE cc_start: 0.7585 (t80) cc_final: 0.7104 (t80)
REVERT: A  280 GLN cc_start: 0.8530 (mt0) cc_final: 0.8109 (mt0)
REVERT: A  289 LEU cc_start: 0.8464 (mt) cc_final: 0.7694 (tp)
REVERT: A  329 GLN cc_start: 0.7470 (mt0) cc_final: 0.6878 (mm110)
REVERT: A  354 LYS cc_start: 0.8649 (tttt) cc_final: 0.8230 (mtpp)
REVERT: A  384 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6987 (mp)
REVERT: A  463 PHE cc_start: 0.7326 (t80) cc_final: 0.7119 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0363
  time to fit residues: 3.4516
Evaluate side-chains
  70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  417 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 22 optimal weight:    0.1980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.143839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.128642 restraints weight = 3742.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.89
r_work: 0.3441 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2852  Z= 0.134
  Angle     :  0.616   7.977   3894  Z= 0.294
  Chirality :  0.042   0.131    471
  Planarity :  0.005   0.050    477
  Dihedral  : 11.126 151.476    428
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 34.27 %
    Favored  : 62.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.17 (0.47), residues: 371
  helix:  1.58 (0.32), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.94 (0.67), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.019   0.001   PHE A 348 
 TRP   0.006   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2852)
  covalent geometry    : angle       0.61624 ( 3894)
  hydrogen bonds       : bond        0.03548 (  227)
  hydrogen bonds       : angle       4.90556 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  268 PHE cc_start: 0.7482 (t80) cc_final: 0.6980 (t80)
REVERT: A  280 GLN cc_start: 0.8519 (mt0) cc_final: 0.8058 (mt0)
REVERT: A  329 GLN cc_start: 0.7388 (mt0) cc_final: 0.6745 (mm110)
REVERT: A  354 LYS cc_start: 0.8626 (tttt) cc_final: 0.8155 (mtpp)
REVERT: A  384 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6638 (mp)
REVERT: A  415 VAL cc_start: 0.8342 (t) cc_final: 0.7898 (p)
REVERT: A  463 PHE cc_start: 0.7071 (t80) cc_final: 0.6814 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0348
  time to fit residues: 3.4060
Evaluate side-chains
  70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  405 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.143890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.127942 restraints weight = 3772.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.96
r_work: 0.3442 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2852  Z= 0.155
  Angle     :  0.640   8.206   3894  Z= 0.303
  Chirality :  0.042   0.122    471
  Planarity :  0.005   0.049    477
  Dihedral  : 11.169 153.960    428
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 36.71 %
    Favored  : 59.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.26 (0.47), residues: 371
  helix:  1.61 (0.32), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.76 (0.70), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.018   0.001   PHE A  27 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 2852)
  covalent geometry    : angle       0.64010 ( 3894)
  hydrogen bonds       : bond        0.03743 (  227)
  hydrogen bonds       : angle       4.93485 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  169 MET cc_start: 0.6837 (ttt) cc_final: 0.6549 (ttt)
REVERT: A  268 PHE cc_start: 0.7469 (t80) cc_final: 0.6977 (t80)
REVERT: A  280 GLN cc_start: 0.8439 (mt0) cc_final: 0.7994 (mt0)
REVERT: A  329 GLN cc_start: 0.7389 (mt0) cc_final: 0.6726 (mm110)
REVERT: A  354 LYS cc_start: 0.8710 (tttt) cc_final: 0.8237 (mtpp)
REVERT: A  384 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6647 (mp)
REVERT: A  415 VAL cc_start: 0.8287 (t) cc_final: 0.7839 (p)
REVERT: A  453 MET cc_start: 0.7634 (mmt) cc_final: 0.7376 (mmt)
REVERT: A  471 ARG cc_start: 0.7995 (ttt90) cc_final: 0.6796 (ttp-170)
  outliers start: 10
  outliers final: 7
  residues processed: 72
  average time/residue: 0.0431
  time to fit residues: 4.0480
Evaluate side-chains
  71 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  405 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   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 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.143618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.127565 restraints weight = 3689.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.91
r_work: 0.3431 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   2852  Z= 0.165
  Angle     :  0.655   9.527   3894  Z= 0.310
  Chirality :  0.042   0.122    471
  Planarity :  0.005   0.049    477
  Dihedral  : 11.219 154.500    428
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 34.97 %
    Favored  : 60.49 %
  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:  1.24 (0.46), residues: 371
  helix:  1.60 (0.32), residues: 301
  sheet:  None (None), residues: 0
  loop : -2.68 (0.69), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.010   0.001   TYR A 422 
 PHE   0.018   0.002   PHE A  27 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 2852)
  covalent geometry    : angle       0.65501 ( 3894)
  hydrogen bonds       : bond        0.03833 (  227)
  hydrogen bonds       : angle       4.96067 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  169 MET cc_start: 0.6873 (ttt) cc_final: 0.6614 (ttt)
REVERT: A  268 PHE cc_start: 0.7507 (t80) cc_final: 0.7024 (t80)
REVERT: A  280 GLN cc_start: 0.8426 (mt0) cc_final: 0.7994 (mt0)
REVERT: A  329 GLN cc_start: 0.7460 (mt0) cc_final: 0.6691 (mm110)
REVERT: A  354 LYS cc_start: 0.8736 (tttt) cc_final: 0.8250 (mtpp)
REVERT: A  384 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6638 (mp)
REVERT: A  415 VAL cc_start: 0.8296 (t) cc_final: 0.7835 (p)
REVERT: A  451 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7518 (m-90)
REVERT: A  453 MET cc_start: 0.7641 (mmt) cc_final: 0.7373 (mmt)
REVERT: A  471 ARG cc_start: 0.8009 (ttt90) cc_final: 0.6819 (ttp-170)
  outliers start: 13
  outliers final: 9
  residues processed: 71
  average time/residue: 0.0397
  time to fit residues: 3.7096
Evaluate side-chains
  74 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  451 TRP
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.137049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.120812 restraints weight = 3970.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 3.09
r_work: 0.3395 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   2852  Z= 0.178
  Angle     :  0.682   9.947   3894  Z= 0.321
  Chirality :  0.043   0.125    471
  Planarity :  0.005   0.049    477
  Dihedral  : 11.281 155.356    428
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 34.62 %
    Favored  : 61.19 %
  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:  1.24 (0.46), residues: 371
  helix:  1.60 (0.32), residues: 301
  sheet:  None (None), residues: 0
  loop : -2.70 (0.70), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 357 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.018   0.002   PHE A  27 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 2852)
  covalent geometry    : angle       0.68168 ( 3894)
  hydrogen bonds       : bond        0.03974 (  227)
  hydrogen bonds       : angle       5.00542 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A  169 MET cc_start: 0.6822 (ttt) cc_final: 0.6614 (ttt)
REVERT: A  268 PHE cc_start: 0.7507 (t80) cc_final: 0.7044 (t80)
REVERT: A  280 GLN cc_start: 0.8347 (mt0) cc_final: 0.7911 (mt0)
REVERT: A  329 GLN cc_start: 0.7576 (mt0) cc_final: 0.6676 (mm-40)
REVERT: A  351 LEU cc_start: 0.7927 (mt) cc_final: 0.7244 (tt)
REVERT: A  354 LYS cc_start: 0.8786 (tttt) cc_final: 0.8310 (mtpp)
REVERT: A  384 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6772 (mp)
REVERT: A  415 VAL cc_start: 0.8274 (t) cc_final: 0.7792 (p)
REVERT: A  451 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.7428 (m-90)
REVERT: A  453 MET cc_start: 0.7631 (mmt) cc_final: 0.7369 (mmt)
REVERT: A  471 ARG cc_start: 0.8032 (ttt90) cc_final: 0.6845 (ttp-170)
  outliers start: 12
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0423
  time to fit residues: 4.2045
Evaluate side-chains
  72 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  451 TRP
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.144032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.128017 restraints weight = 3820.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 3.01
r_work: 0.3377 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2852  Z= 0.162
  Angle     :  0.697  11.641   3894  Z= 0.326
  Chirality :  0.043   0.123    471
  Planarity :  0.005   0.048    477
  Dihedral  : 11.030 155.737    426
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 34.62 %
    Favored  : 60.49 %
  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:  1.13 (0.46), residues: 371
  helix:  1.48 (0.31), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.61 (0.73), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.017   0.002   PHE A  27 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 2852)
  covalent geometry    : angle       0.69728 ( 3894)
  hydrogen bonds       : bond        0.03868 (  227)
  hydrogen bonds       : angle       5.00636 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  169 MET cc_start: 0.6787 (ttt) cc_final: 0.6575 (ttt)
REVERT: A  268 PHE cc_start: 0.7500 (t80) cc_final: 0.7062 (t80)
REVERT: A  280 GLN cc_start: 0.8354 (mt0) cc_final: 0.7902 (mt0)
REVERT: A  329 GLN cc_start: 0.7564 (mt0) cc_final: 0.6662 (mm-40)
REVERT: A  354 LYS cc_start: 0.8765 (tttt) cc_final: 0.8293 (mtpp)
REVERT: A  384 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6811 (mp)
REVERT: A  415 VAL cc_start: 0.8306 (t) cc_final: 0.7827 (p)
REVERT: A  451 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.7421 (m-90)
REVERT: A  471 ARG cc_start: 0.8042 (ttt90) cc_final: 0.6916 (ttp-170)
  outliers start: 14
  outliers final: 9
  residues processed: 67
  average time/residue: 0.0420
  time to fit residues: 3.7068
Evaluate side-chains
  72 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  166 PHE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  451 TRP
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0270
   overall best weight:    0.6640

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.143462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.127519 restraints weight = 3763.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.97
r_work: 0.3427 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2852  Z= 0.170
  Angle     :  0.720  10.695   3894  Z= 0.333
  Chirality :  0.044   0.204    471
  Planarity :  0.005   0.048    477
  Dihedral  : 10.951 156.238    426
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 36.01 %
    Favored  : 60.49 %
  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:  1.27 (0.46), residues: 371
  helix:  1.59 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop : -2.52 (0.71), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.013   0.001   TYR A 422 
 PHE   0.018   0.002   PHE A  27 
 TRP   0.006   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 2852)
  covalent geometry    : angle       0.71960 ( 3894)
  hydrogen bonds       : bond        0.03926 (  227)
  hydrogen bonds       : angle       5.00200 (  669)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  268 PHE cc_start: 0.7538 (t80) cc_final: 0.7109 (t80)
REVERT: A  280 GLN cc_start: 0.8321 (mt0) cc_final: 0.7860 (mt0)
REVERT: A  329 GLN cc_start: 0.7619 (mt0) cc_final: 0.6694 (mm-40)
REVERT: A  354 LYS cc_start: 0.8772 (tttt) cc_final: 0.8303 (mtpp)
REVERT: A  384 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6813 (mp)
REVERT: A  415 VAL cc_start: 0.8304 (t) cc_final: 0.7825 (p)
REVERT: A  451 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.7415 (m-90)
REVERT: A  471 ARG cc_start: 0.8034 (ttt90) cc_final: 0.6921 (ttp-170)
  outliers start: 10
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0431
  time to fit residues: 4.0035
Evaluate side-chains
  75 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  451 TRP
Chi-restraints excluded: chain A residue  455 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0670
   chunk 4 optimal weight:    0.7980
   chunk 34 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.142633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.126971 restraints weight = 3710.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.95
r_work: 0.3453 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
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      :  0.003   0.039   2852  Z= 0.148
  Angle     :  0.677   9.879   3894  Z= 0.317
  Chirality :  0.042   0.122    471
  Planarity :  0.005   0.048    477
  Dihedral  : 10.953 156.614    426
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 37.41 %
    Favored  : 58.74 %
  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:  1.36 (0.46), residues: 371
  helix:  1.72 (0.31), residues: 298
  sheet:  None (None), residues: 0
  loop : -2.62 (0.68), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.016   0.002   PHE A  27 
 TRP   0.006   0.001   TRP A 451 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2852)
  covalent geometry    : angle       0.67709 ( 3894)
  hydrogen bonds       : bond        0.03724 (  227)
  hydrogen bonds       : angle       4.96617 (  669)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 750.20 seconds
wall clock time: 13 minutes 34.02 seconds (814.02 seconds total)