Starting phenix.real_space_refine
on Wed Jul 23 15:55:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jjl_36360/07_2025/8jjl_36360_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jjl_36360/07_2025/8jjl_36360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jjl_36360/07_2025/8jjl_36360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jjl_36360/07_2025/8jjl_36360.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jjl_36360/07_2025/8jjl_36360_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jjl_36360/07_2025/8jjl_36360_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 707 atoms to isotropic.
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      20      5.16       5
     C    1986      2.51       5
     N     488      2.21       5
     O     532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3026
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2998
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 8, 'TRANS': 366}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'DZQ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.78, per 1000 atoms: 0.92
  Number of scatterers: 3026
  At special positions: 0
  Unit cell: (55.76, 96.76, 92.66, 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      20     16.00
     O     532      8.00
     N     488      7.00
     C    1986      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 381.6 milliseconds
  

  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:  722

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 0 sheets defined
      89.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 61
      removed outlier: 3.542A  pdb=" N   VAL A  33 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 96
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 102 through 133
    Processing helix  chain 'A' and resid 137 through 145
      removed outlier: 3.665A  pdb=" N   SER A 143 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 171
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 3.618A  pdb=" N   ILE A 182 " --> pdb=" O   HIS A 178 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 208
      removed outlier: 4.571A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 249
      removed outlier: 3.502A  pdb=" N   THR A 239 " --> pdb=" O   ASP A 235 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 240 " --> pdb=" O   ASN A 236 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LYS A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 273
      removed outlier: 4.386A  pdb=" N   VAL A 256 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 303
      removed outlier: 3.761A  pdb=" N   PHE A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASP A 289 " --> pdb=" O   ARG A 285 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 314
      removed outlier: 3.689A  pdb=" N   ALA A 312 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 366
      removed outlier: 3.934A  pdb=" N   THR A 319 " --> pdb=" O   GLU A 315 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 327 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
      Proline residue:  A 355  - end of helix
      removed outlier: 4.067A  pdb=" N   GLN A 366 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 385
    Processing helix  chain 'A' and resid 387 through 394
      removed outlier: 4.022A  pdb=" N   LEU A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 407

    244 hydrogen bonds defined for protein.
    732 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: 0.75

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 478
        1.31 -     1.44: 851
        1.44 -     1.56: 1735
        1.56 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 3095
  Sorted by residual:
  bond pdb=" C21 DZQ A 501 "
       pdb=" O22 DZQ A 501 "
    ideal  model  delta    sigma   weight residual
    1.362  1.455 -0.093 2.00e-02 2.50e+03 2.17e+01
  bond pdb=" C   TYR A 328 "
       pdb=" O   TYR A 328 "
    ideal  model  delta    sigma   weight residual
    1.237  1.187  0.050 1.16e-02 7.43e+03 1.86e+01
  bond pdb=" C   ILE A 325 "
       pdb=" O   ILE A 325 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.19e-02 7.06e+03 1.34e+01
  bond pdb=" C24 DZQ A 501 "
       pdb=" N26 DZQ A 501 "
    ideal  model  delta    sigma   weight residual
    1.354  1.415 -0.061 2.00e-02 2.50e+03 9.21e+00
  bond pdb=" C20 DZQ A 501 "
       pdb=" N26 DZQ A 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.447 -0.053 2.00e-02 2.50e+03 6.89e+00
  ... (remaining 3090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 4014
        1.63 -     3.26: 147
        3.26 -     4.88: 32
        4.88 -     6.51: 8
        6.51 -     8.14: 4
  Bond angle restraints: 4205
  Sorted by residual:
  angle pdb=" N   ILE A 325 "
        pdb=" CA  ILE A 325 "
        pdb=" C   ILE A 325 "
      ideal   model   delta    sigma   weight residual
     110.72  102.58    8.14 1.01e+00 9.80e-01 6.49e+01
  angle pdb=" N   LEU A 329 "
        pdb=" CA  LEU A 329 "
        pdb=" C   LEU A 329 "
      ideal   model   delta    sigma   weight residual
     111.11  104.67    6.44 1.20e+00 6.94e-01 2.88e+01
  angle pdb=" O   ALA A 323 "
        pdb=" C   ALA A 323 "
        pdb=" N   TYR A 324 "
      ideal   model   delta    sigma   weight residual
     122.33  129.34   -7.01 1.34e+00 5.57e-01 2.74e+01
  angle pdb=" CA  ALA A 323 "
        pdb=" C   ALA A 323 "
        pdb=" N   TYR A 324 "
      ideal   model   delta    sigma   weight residual
     117.82  110.85    6.97 1.42e+00 4.96e-01 2.41e+01
  angle pdb=" N   LYS A 334 "
        pdb=" CA  LYS A 334 "
        pdb=" C   LYS A 334 "
      ideal   model   delta    sigma   weight residual
     111.82  107.63    4.19 1.16e+00 7.43e-01 1.30e+01
  ... (remaining 4200 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.88: 1605
       15.88 -    31.76: 181
       31.76 -    47.64: 37
       47.64 -    63.52: 8
       63.52 -    79.40: 5
  Dihedral angle restraints: 1836
    sinusoidal: 728
      harmonic: 1108
  Sorted by residual:
  dihedral pdb=" CA  HIS A 178 "
           pdb=" C   HIS A 178 "
           pdb=" N   GLN A 179 "
           pdb=" CA  GLN A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.84  -21.16     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" C   TYR A 324 "
           pdb=" N   TYR A 324 "
           pdb=" CA  TYR A 324 "
           pdb=" CB  TYR A 324 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.22   -9.38     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" CA  ASP A 367 "
           pdb=" C   ASP A 367 "
           pdb=" N   ASN A 368 "
           pdb=" CA  ASN A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.83   18.17     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 1833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 400
       0.055 -    0.110: 77
       0.110 -    0.165: 7
       0.165 -    0.220: 3
       0.220 -    0.275: 1
  Chirality restraints: 488
  Sorted by residual:
  chirality pdb=" CA  TYR A 324 "
            pdb=" N   TYR A 324 "
            pdb=" C   TYR A 324 "
            pdb=" CB  TYR A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  LEU A 233 "
            pdb=" N   LEU A 233 "
            pdb=" C   LEU A 233 "
            pdb=" CB  LEU A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  ILE A 325 "
            pdb=" CA  ILE A 325 "
            pdb=" CG1 ILE A 325 "
            pdb=" CG2 ILE A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.45e-01
  ... (remaining 485 not shown)

  Planarity restraints: 515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 323 "   -0.023 2.00e-02 2.50e+03   5.18e-02 2.68e+01
        pdb=" C   ALA A 323 "    0.089 2.00e-02 2.50e+03
        pdb=" O   ALA A 323 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   TYR A 324 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 227 "    0.022 2.00e-02 2.50e+03   4.40e-02 1.93e+01
        pdb=" C   LYS A 227 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   LYS A 227 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ARG A 228 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 206 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   VAL A 206 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   VAL A 206 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER A 207 "    0.015 2.00e-02 2.50e+03
  ... (remaining 512 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 102
        2.72 -     3.26: 3413
        3.26 -     3.81: 5334
        3.81 -     4.35: 6239
        4.35 -     4.90: 10361
  Nonbonded interactions: 25449
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 113 "
            pdb=" OH  TYR A 383 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OH  TYR A 219 "
            pdb=" O   LEU A 339 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" NZ  LYS A 257 "
            pdb=" OD1 ASN A 303 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   PHE A 139 "
            pdb=" OG  SER A 143 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG1 THR A 118 "
            pdb=" OG  SER A 207 "
     model   vdw
     2.338 3.040
  ... (remaining 25444 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:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.280
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
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   3097  Z= 0.285
  Angle     :  0.766   8.138   4209  Z= 0.494
  Chirality :  0.045   0.275    488
  Planarity :  0.005   0.052    515
  Dihedral  : 14.230  79.405   1108
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  0.93 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.46), residues: 371
  helix:  1.35 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.68 (0.85), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 380 
 HIS   0.005   0.001   HIS A 178 
 PHE   0.008   0.001   PHE A 357 
 TYR   0.031   0.002   TYR A 328 
 ARG   0.001   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17535 (  244)
  hydrogen bonds       : angle       5.98802 (  732)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       0.49006 (    4)
  covalent geometry    : bond        0.00469 ( 3095)
  covalent geometry    : angle       0.76650 ( 4205)

*********************** 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
  102 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.7041 (m-10) cc_final: 0.6517 (m-10)
REVERT: A   82 MET cc_start: 0.7587 (tmm) cc_final: 0.6999 (ttp)
REVERT: A  151 ARG cc_start: 0.6157 (tpm170) cc_final: 0.5952 (tpm170)
  outliers start: 5
  outliers final: 3
  residues processed: 101
  average time/residue: 0.1413
  time to fit residues: 17.2125
Evaluate side-chains
  75 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  324 TYR
Chi-restraints excluded: chain A residue  327 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0970
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 311 GLN
A 363 HIS
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.149272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.117805 restraints weight = 4273.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.48
r_work: 0.3414 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3097  Z= 0.156
  Angle     :  0.581   6.547   4209  Z= 0.311
  Chirality :  0.039   0.118    488
  Planarity :  0.004   0.043    515
  Dihedral  :  6.373  44.618    430
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 11.46 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.44), residues: 371
  helix:  1.11 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -0.03 (1.01), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.020   0.002   PHE A  61 
 TYR   0.020   0.002   TYR A 328 
 ARG   0.002   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04940 (  244)
  hydrogen bonds       : angle       4.48179 (  732)
  SS BOND              : bond        0.00377 (    2)
  SS BOND              : angle       0.71718 (    4)
  covalent geometry    : bond        0.00335 ( 3095)
  covalent geometry    : angle       0.58055 ( 4205)

*********************** 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
  97 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7300 (m-10) cc_final: 0.6202 (m-10)
REVERT: A   82 MET cc_start: 0.7943 (tmm) cc_final: 0.7246 (ttp)
REVERT: A  135 ILE cc_start: 0.8102 (mm) cc_final: 0.7835 (mm)
REVERT: A  223 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7068 (m-80)
REVERT: A  238 GLU cc_start: 0.8386 (tt0) cc_final: 0.7892 (tp30)
REVERT: A  328 TYR cc_start: 0.6878 (t80) cc_final: 0.6132 (t80)
REVERT: A  332 CYS cc_start: 0.8296 (t) cc_final: 0.7909 (m)
  outliers start: 11
  outliers final: 4
  residues processed: 88
  average time/residue: 0.1382
  time to fit residues: 15.3712
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.147655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.115740 restraints weight = 4218.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.49
r_work: 0.3384 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3097  Z= 0.165
  Angle     :  0.606  11.104   4209  Z= 0.320
  Chirality :  0.040   0.234    488
  Planarity :  0.003   0.034    515
  Dihedral  :  5.405  40.032    422
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 12.69 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.44), residues: 371
  helix:  1.34 (0.29), residues: 311
  sheet:  None (None), residues: 0
  loop : -0.23 (0.94), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 237 
 HIS   0.002   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.020   0.002   TYR A 328 
 ARG   0.001   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04884 (  244)
  hydrogen bonds       : angle       4.41404 (  732)
  SS BOND              : bond        0.00710 (    2)
  SS BOND              : angle       3.61425 (    4)
  covalent geometry    : bond        0.00366 ( 3095)
  covalent geometry    : angle       0.59608 ( 4205)

*********************** 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
  92 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8013 (tmm) cc_final: 0.7398 (ttp)
REVERT: A  223 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7060 (m-80)
REVERT: A  238 GLU cc_start: 0.8428 (tt0) cc_final: 0.7862 (tp30)
REVERT: A  328 TYR cc_start: 0.6972 (t80) cc_final: 0.6060 (t80)
REVERT: A  332 CYS cc_start: 0.8314 (t) cc_final: 0.7699 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 85
  average time/residue: 0.1207
  time to fit residues: 12.9296
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9990
   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 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.147839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.115260 restraints weight = 4283.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.55
r_work: 0.3378 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3097  Z= 0.147
  Angle     :  0.577   8.747   4209  Z= 0.304
  Chirality :  0.039   0.197    488
  Planarity :  0.003   0.026    515
  Dihedral  :  5.341  43.758    422
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.79 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.44), residues: 371
  helix:  1.54 (0.29), residues: 306
  sheet:  None (None), residues: 0
  loop : -0.31 (0.90), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.024   0.002   TYR A 324 
 ARG   0.001   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04655 (  244)
  hydrogen bonds       : angle       4.30497 (  732)
  SS BOND              : bond        0.00236 (    2)
  SS BOND              : angle       2.89242 (    4)
  covalent geometry    : bond        0.00320 ( 3095)
  covalent geometry    : angle       0.56990 ( 4205)

*********************** 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
  89 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8032 (tmm) cc_final: 0.7435 (ttp)
REVERT: A  223 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7067 (m-80)
REVERT: A  238 GLU cc_start: 0.8501 (tt0) cc_final: 0.7917 (tp30)
REVERT: A  308 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8724 (mmmt)
REVERT: A  328 TYR cc_start: 0.7243 (t80) cc_final: 0.6274 (t80)
REVERT: A  332 CYS cc_start: 0.8265 (t) cc_final: 0.7743 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 83
  average time/residue: 0.1288
  time to fit residues: 13.4052
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.147412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.114912 restraints weight = 4258.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.50
r_work: 0.3378 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3097  Z= 0.145
  Angle     :  0.575   7.373   4209  Z= 0.301
  Chirality :  0.038   0.168    488
  Planarity :  0.003   0.024    515
  Dihedral  :  5.212  45.601    422
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 17.65 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.44), residues: 371
  helix:  1.65 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.61 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.033   0.002   TYR A 324 
 ARG   0.001   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04609 (  244)
  hydrogen bonds       : angle       4.25198 (  732)
  SS BOND              : bond        0.00592 (    2)
  SS BOND              : angle       2.69132 (    4)
  covalent geometry    : bond        0.00315 ( 3095)
  covalent geometry    : angle       0.56913 ( 4205)

*********************** 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
  94 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.6695 (ttt) cc_final: 0.6337 (ttt)
REVERT: A   82 MET cc_start: 0.8076 (tmm) cc_final: 0.7464 (ttp)
REVERT: A  223 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7113 (m-80)
REVERT: A  238 GLU cc_start: 0.8461 (tt0) cc_final: 0.7882 (tp30)
REVERT: A  308 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8752 (mmmt)
REVERT: A  328 TYR cc_start: 0.7290 (t80) cc_final: 0.6374 (t80)
REVERT: A  332 CYS cc_start: 0.8256 (t) cc_final: 0.7782 (m)
REVERT: A  333 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7495 (mp)
  outliers start: 14
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1259
  time to fit residues: 13.5688
Evaluate side-chains
  85 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0010
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.1980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.149150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.118497 restraints weight = 4373.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.44
r_work: 0.3412 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3097  Z= 0.128
  Angle     :  0.569   7.543   4209  Z= 0.293
  Chirality :  0.037   0.143    488
  Planarity :  0.003   0.022    515
  Dihedral  :  5.347  48.693    422
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.20 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.45), residues: 371
  helix:  1.69 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.72 (0.86), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.034   0.002   TYR A 324 
 ARG   0.001   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04447 (  244)
  hydrogen bonds       : angle       4.19940 (  732)
  SS BOND              : bond        0.00082 (    2)
  SS BOND              : angle       2.72174 (    4)
  covalent geometry    : bond        0.00269 ( 3095)
  covalent geometry    : angle       0.56294 ( 4205)

*********************** 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
  87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7965 (tmm) cc_final: 0.7403 (ttp)
REVERT: A   96 MET cc_start: 0.7466 (mtt) cc_final: 0.6707 (mmm)
REVERT: A  223 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7140 (m-80)
REVERT: A  300 LYS cc_start: 0.8817 (tptm) cc_final: 0.7856 (ttpp)
  outliers start: 14
  outliers final: 9
  residues processed: 78
  average time/residue: 0.1177
  time to fit residues: 11.7206
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.147937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.115227 restraints weight = 4331.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.57
r_work: 0.3372 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3097  Z= 0.146
  Angle     :  0.573   5.660   4209  Z= 0.296
  Chirality :  0.038   0.138    488
  Planarity :  0.003   0.022    515
  Dihedral  :  5.246  46.697    422
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.27 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.45), residues: 371
  helix:  1.63 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.68 (0.89), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.033   0.002   TYR A 324 
 ARG   0.001   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04491 (  244)
  hydrogen bonds       : angle       4.18633 (  732)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       2.51613 (    4)
  covalent geometry    : bond        0.00321 ( 3095)
  covalent geometry    : angle       0.56768 ( 4205)

*********************** 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
  83 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   36 MET cc_start: 0.6714 (ttt) cc_final: 0.6461 (ttt)
REVERT: A   82 MET cc_start: 0.7903 (tmm) cc_final: 0.7434 (ttp)
REVERT: A   96 MET cc_start: 0.7513 (mtt) cc_final: 0.6748 (mmm)
REVERT: A  223 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7157 (m-80)
REVERT: A  238 GLU cc_start: 0.8448 (tt0) cc_final: 0.7911 (tp30)
REVERT: A  300 LYS cc_start: 0.8828 (tptm) cc_final: 0.7803 (ttpt)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1257
  time to fit residues: 12.0673
Evaluate side-chains
  79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0770
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.149094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.117673 restraints weight = 4294.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.45
r_work: 0.3407 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3097  Z= 0.127
  Angle     :  0.561   5.557   4209  Z= 0.291
  Chirality :  0.038   0.130    488
  Planarity :  0.003   0.023    515
  Dihedral  :  5.242  48.534    422
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 17.34 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.45), residues: 371
  helix:  1.66 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.63 (0.89), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.037   0.002   TYR A 324 
 ARG   0.002   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  244)
  hydrogen bonds       : angle       4.16833 (  732)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       2.39297 (    4)
  covalent geometry    : bond        0.00268 ( 3095)
  covalent geometry    : angle       0.55647 ( 4205)

*********************** 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
  82 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   36 MET cc_start: 0.6872 (ttt) cc_final: 0.6618 (ttt)
REVERT: A   82 MET cc_start: 0.7950 (tmm) cc_final: 0.7399 (ttp)
REVERT: A   96 MET cc_start: 0.7480 (mtt) cc_final: 0.6710 (mmm)
REVERT: A  223 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7156 (m-80)
REVERT: A  285 ARG cc_start: 0.6523 (mpt180) cc_final: 0.6317 (mpt180)
REVERT: A  300 LYS cc_start: 0.8779 (tptm) cc_final: 0.7741 (ttpp)
  outliers start: 13
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1110
  time to fit residues: 10.7513
Evaluate side-chains
  75 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.147542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.114387 restraints weight = 4350.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.59
r_work: 0.3361 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3097  Z= 0.150
  Angle     :  0.590   7.453   4209  Z= 0.303
  Chirality :  0.038   0.124    488
  Planarity :  0.003   0.021    515
  Dihedral  :  5.145  44.869    422
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.20 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.45), residues: 371
  helix:  1.67 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.65 (0.87), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.012   0.001   PHE A 208 
 TYR   0.037   0.003   TYR A 324 
 ARG   0.001   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04430 (  244)
  hydrogen bonds       : angle       4.15568 (  732)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       2.46943 (    4)
  covalent geometry    : bond        0.00332 ( 3095)
  covalent geometry    : angle       0.58496 ( 4205)

*********************** 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
  78 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   36 MET cc_start: 0.6892 (ttt) cc_final: 0.6620 (ttt)
REVERT: A   82 MET cc_start: 0.7956 (tmm) cc_final: 0.7500 (ttp)
REVERT: A   96 MET cc_start: 0.7480 (mtt) cc_final: 0.6737 (mmm)
REVERT: A  223 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7133 (m-80)
REVERT: A  300 LYS cc_start: 0.8741 (tptm) cc_final: 0.7677 (ttmt)
  outliers start: 11
  outliers final: 9
  residues processed: 72
  average time/residue: 0.1256
  time to fit residues: 11.3077
Evaluate side-chains
  78 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Chi-restraints excluded: chain A residue  405 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 30 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0570
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.148816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.116035 restraints weight = 4196.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.54
r_work: 0.3387 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3097  Z= 0.135
  Angle     :  0.581   7.012   4209  Z= 0.300
  Chirality :  0.038   0.127    488
  Planarity :  0.003   0.022    515
  Dihedral  :  5.158  46.370    422
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.58 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.45), residues: 371
  helix:  1.65 (0.29), residues: 303
  sheet:  None (None), residues: 0
  loop : -0.50 (0.91), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.013   0.001   PHE A 208 
 TYR   0.038   0.003   TYR A 324 
 ARG   0.001   0.000   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  244)
  hydrogen bonds       : angle       4.12706 (  732)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       2.38186 (    4)
  covalent geometry    : bond        0.00290 ( 3095)
  covalent geometry    : angle       0.57665 ( 4205)

********************** 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
  80 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   36 MET cc_start: 0.6843 (ttt) cc_final: 0.6597 (ttt)
REVERT: A   82 MET cc_start: 0.7936 (tmm) cc_final: 0.7409 (ttp)
REVERT: A   96 MET cc_start: 0.7495 (mtt) cc_final: 0.6745 (mmm)
REVERT: A  223 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7127 (m-80)
REVERT: A  300 LYS cc_start: 0.8697 (tptm) cc_final: 0.7593 (ttmt)
  outliers start: 11
  outliers final: 9
  residues processed: 74
  average time/residue: 0.1231
  time to fit residues: 11.4559
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Chi-restraints excluded: chain A residue  405 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0270
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.149302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.116989 restraints weight = 4373.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.52
r_work: 0.3407 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3097  Z= 0.133
  Angle     :  0.588   6.277   4209  Z= 0.306
  Chirality :  0.038   0.128    488
  Planarity :  0.003   0.022    515
  Dihedral  :  5.134  47.679    422
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.58 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.45), residues: 371
  helix:  1.70 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -0.52 (0.90), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.013   0.001   PHE A 208 
 TYR   0.036   0.002   TYR A 324 
 ARG   0.000   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  244)
  hydrogen bonds       : angle       4.10826 (  732)
  SS BOND              : bond        0.00109 (    2)
  SS BOND              : angle       2.46759 (    4)
  covalent geometry    : bond        0.00287 ( 3095)
  covalent geometry    : angle       0.58350 ( 4205)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1902.73 seconds
wall clock time: 33 minutes 27.92 seconds (2007.92 seconds total)