Starting phenix.real_space_refine
on Sat Apr 26 16:21:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zrt_60404/04_2025/8zrt_60404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zrt_60404/04_2025/8zrt_60404.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zrt_60404/04_2025/8zrt_60404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zrt_60404/04_2025/8zrt_60404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zrt_60404/04_2025/8zrt_60404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zrt_60404/04_2025/8zrt_60404.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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      21      5.16       5
     C    1545      2.51       5
     N     363      2.21       5
     O     393      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2322
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2158
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 12, 'TRANS': 269}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 66
    Chain: "L"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 164
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 20}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.34, per 1000 atoms: 1.01
  Number of scatterers: 2322
  At special positions: 0
  Unit cell: (60.69, 71.4, 79.73, 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      21     16.00
     O     393      8.00
     N     363      7.00
     C    1545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 174 " - pdb=" SG  CYS R 255 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   1 " - pdb=" SG  CYS L  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   3 " - pdb=" SG  CYS L  11 " 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: 0.62
  Conformation dependent library (CDL) restraints added in 304.3 milliseconds
  

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  586

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 2 sheets defined
      80.9% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'R' and resid 97 through 128
      removed outlier: 3.870A  pdb=" N   VAL R 106 " --> pdb=" O   TYR R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 164
      Proline residue:  R 156  - end of helix
      removed outlier: 3.837A  pdb=" N   LEU R 162 " --> pdb=" O   ASN R 158 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LEU R 163 " --> pdb=" O   VAL R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 170 through 205
      Proline residue:  R 178  - end of helix
      removed outlier: 3.796A  pdb=" N   VAL R 203 " --> pdb=" O   ARG R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 238
      removed outlier: 3.698A  pdb=" N   LEU R 224 " --> pdb=" O   VAL R 220 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL R 230 " --> pdb=" O   TRP R 226 " (cutoff:3.500A)
      Proline residue:  R 235  - end of helix
      removed outlier: 3.695A  pdb=" N   ILE R 238 " --> pdb=" O   VAL R 234 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 272
      removed outlier: 3.511A  pdb=" N   GLN R 267 " --> pdb=" O   THR R 263 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ALA R 272 " --> pdb=" O   PHE R 268 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 301
      removed outlier: 4.471A  pdb=" N   LEU R 284 " --> pdb=" O   PHE R 280 " (cutoff:3.500A)
      Proline residue:  R 285  - end of helix
    Processing helix  chain 'R' and resid 319 through 349
      Proline residue:  R 338  - end of helix
    Processing helix  chain 'R' and resid 356 through 388
      removed outlier: 3.884A  pdb=" N   ASN R 382 " --> pdb=" O   ASN R 378 " (cutoff:3.500A)
      Proline residue:  R 383  - end of helix
    Processing helix  chain 'R' and resid 390 through 399
      removed outlier: 3.704A  pdb=" N   SER R 399 " --> pdb=" O   ASN R 395 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 10 through 18
    Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 243
    Processing sheet with id=AA2, first strand: chain 'R' and resid 246 through 247

    181 hydrogen bonds defined for protein.
    537 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: 0.61

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 693
        1.34 -     1.46: 576
        1.46 -     1.58: 1080
        1.58 -     1.70: 0
        1.70 -     1.81: 27
  Bond restraints: 2376
  Sorted by residual:
  bond pdb=" CB  ASP R 147 "
       pdb=" CG  ASP R 147 "
    ideal  model  delta    sigma   weight residual
    1.516  1.482  0.034 2.50e-02 1.60e+03 1.82e+00
  bond pdb=" C   ILE R 222 "
       pdb=" O   ILE R 222 "
    ideal  model  delta    sigma   weight residual
    1.233  1.243 -0.010 1.22e-02 6.72e+03 6.90e-01
  bond pdb=" CA  ASN R 373 "
       pdb=" C   ASN R 373 "
    ideal  model  delta    sigma   weight residual
    1.524  1.514  0.010 1.28e-02 6.10e+03 6.36e-01
  bond pdb=" CB  PRO R  93 "
       pdb=" CG  PRO R  93 "
    ideal  model  delta    sigma   weight residual
    1.492  1.530 -0.038 5.00e-02 4.00e+02 5.91e-01
  bond pdb=" C   VAL R 234 "
       pdb=" N   PRO R 235 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.28e-02 6.10e+03 5.23e-01
  ... (remaining 2371 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 3149
        1.70 -     3.40: 74
        3.40 -     5.10: 13
        5.10 -     6.80: 6
        6.80 -     8.50: 3
  Bond angle restraints: 3245
  Sorted by residual:
  angle pdb=" CA  PRO R  93 "
        pdb=" N   PRO R  93 "
        pdb=" CD  PRO R  93 "
      ideal   model   delta    sigma   weight residual
     112.00  106.33    5.67 1.40e+00 5.10e-01 1.64e+01
  angle pdb=" C   VAL R 234 "
        pdb=" CA  VAL R 234 "
        pdb=" CB  VAL R 234 "
      ideal   model   delta    sigma   weight residual
     113.70  110.87    2.83 9.50e-01 1.11e+00 8.87e+00
  angle pdb=" C   ASN R 373 "
        pdb=" N   MET R 374 "
        pdb=" CA  MET R 374 "
      ideal   model   delta    sigma   weight residual
     121.58  116.12    5.46 1.95e+00 2.63e-01 7.85e+00
  angle pdb=" N   GLY R  92 "
        pdb=" CA  GLY R  92 "
        pdb=" C   GLY R  92 "
      ideal   model   delta    sigma   weight residual
     112.34  117.90   -5.56 2.04e+00 2.40e-01 7.42e+00
  angle pdb=" CB  MET R 374 "
        pdb=" CG  MET R 374 "
        pdb=" SD  MET R 374 "
      ideal   model   delta    sigma   weight residual
     112.70  104.75    7.95 3.00e+00 1.11e-01 7.02e+00
  ... (remaining 3240 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 1229
       17.96 -    35.92: 127
       35.92 -    53.88: 39
       53.88 -    71.84: 4
       71.84 -    89.80: 2
  Dihedral angle restraints: 1401
    sinusoidal: 506
      harmonic: 895
  Sorted by residual:
  dihedral pdb=" CB  CYS L   1 "
           pdb=" SG  CYS L   1 "
           pdb=" SG  CYS L  15 "
           pdb=" CB  CYS L  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.24   50.24     1      1.00e+01 1.00e-02 3.46e+01
  dihedral pdb=" CA  MET R 374 "
           pdb=" C   MET R 374 "
           pdb=" N   ALA R 375 "
           pdb=" CA  ALA R 375 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.28   16.72     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CB  GLU R 299 "
           pdb=" CG  GLU R 299 "
           pdb=" CD  GLU R 299 "
           pdb=" OE1 GLU R 299 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.80  -89.80     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 1398 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 301
       0.043 -    0.086: 83
       0.086 -    0.129: 14
       0.129 -    0.172: 3
       0.172 -    0.215: 1
  Chirality restraints: 402
  Sorted by residual:
  chirality pdb=" CB  ILE R 187 "
            pdb=" CA  ILE R 187 "
            pdb=" CG1 ILE R 187 "
            pdb=" CG2 ILE R 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  MET R 374 "
            pdb=" N   MET R 374 "
            pdb=" C   MET R 374 "
            pdb=" CB  MET R 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.94e-01
  chirality pdb=" CA  PRO R 338 "
            pdb=" N   PRO R 338 "
            pdb=" C   PRO R 338 "
            pdb=" CB  PRO R 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 399 not shown)

  Planarity restraints: 388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R  92 "    0.102 5.00e-02 4.00e+02   1.52e-01 3.71e+01
        pdb=" N   PRO R  93 "   -0.263 5.00e-02 4.00e+02
        pdb=" CA  PRO R  93 "    0.083 5.00e-02 4.00e+02
        pdb=" CD  PRO R  93 "    0.079 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 372 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.60e+00
        pdb=" C   ILE R 372 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ILE R 372 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN R 373 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 366 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.97e+00
        pdb=" C   VAL R 366 "    0.034 2.00e-02 2.50e+03
        pdb=" O   VAL R 366 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU R 367 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 385 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 421
        2.76 -     3.30: 2406
        3.30 -     3.83: 3994
        3.83 -     4.37: 4137
        4.37 -     4.90: 7507
  Nonbonded interactions: 18465
  Sorted by model distance:
  nonbonded pdb=" O   PRO R 285 "
            pdb=" OG1 THR R 289 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OD1 ASN R 134 "
            pdb=" ND2 ASN R 137 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   SER R 376 "
            pdb=" OG  SER R 379 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ASP R 154 "
            pdb=" ND2 ASN R 158 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" O   GLU R 165 "
            pdb=" NE2 HIS L  16 "
     model   vdw
     2.315 3.120
  ... (remaining 18460 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.650
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2380  Z= 0.155
  Angle     :  0.695   8.503   3253  Z= 0.364
  Chirality :  0.041   0.215    402
  Planarity :  0.009   0.152    388
  Dihedral  : 16.251  89.801    803
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 33.06 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.48), residues: 293
  helix:  0.89 (0.34), residues: 228
  sheet:  None (None), residues: 0
  loop : -3.20 (0.64), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 276 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.013   0.001   PHE R 100 
 TYR   0.008   0.001   TYR R 269 
 ARG   0.004   0.001   ARG R 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12312 (  181)
  hydrogen bonds       : angle       6.17515 (  537)
  SS BOND              : bond        0.00281 (    4)
  SS BOND              : angle       1.22491 (    8)
  covalent geometry    : bond        0.00334 ( 2376)
  covalent geometry    : angle       0.69343 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.250 
Fit side-chains
REVERT: R  236 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7026 (tp30)
REVERT: R  266 MET cc_start: 0.7246 (tpp) cc_final: 0.6853 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 56
  average time/residue: 0.1000
  time to fit residues: 7.1035
Evaluate side-chains
  53 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  386 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R 181 GLN
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 373 ASN
R 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.200779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188492 restraints weight = 3084.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.192285 restraints weight = 1596.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.194837 restraints weight = 946.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.0889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2380  Z= 0.154
  Angle     :  0.648  11.099   3253  Z= 0.326
  Chirality :  0.041   0.207    402
  Planarity :  0.007   0.122    388
  Dihedral  :  4.940  47.557    319
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 26.61 %
    Favored  : 67.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.48), residues: 293
  helix:  1.35 (0.33), residues: 229
  sheet:  None (None), residues: 0
  loop : -3.27 (0.63), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  21 
 HIS   0.003   0.001   HIS L  16 
 PHE   0.011   0.001   PHE R 397 
 TYR   0.008   0.001   TYR R 281 
 ARG   0.002   0.000   ARG R 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04681 (  181)
  hydrogen bonds       : angle       4.45219 (  537)
  SS BOND              : bond        0.00555 (    4)
  SS BOND              : angle       1.09308 (    8)
  covalent geometry    : bond        0.00342 ( 2376)
  covalent geometry    : angle       0.64603 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.248 
Fit side-chains
REVERT: R  236 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7027 (tp30)
REVERT: R  266 MET cc_start: 0.7336 (tpp) cc_final: 0.7011 (mmm)
  outliers start: 14
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0990
  time to fit residues: 8.2122
Evaluate side-chains
  62 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  379 SER
Chi-restraints excluded: chain R residue  386 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 378 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.201651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.189276 restraints weight = 3060.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.193042 restraints weight = 1621.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.195566 restraints weight = 964.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2380  Z= 0.142
  Angle     :  0.634  10.567   3253  Z= 0.321
  Chirality :  0.041   0.208    402
  Planarity :  0.007   0.108    388
  Dihedral  :  4.987  48.743    319
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  9.68 %
    Allowed  : 24.60 %
    Favored  : 65.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.48), residues: 293
  helix:  1.48 (0.33), residues: 229
  sheet:  None (None), residues: 0
  loop : -3.40 (0.62), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 276 
 HIS   0.002   0.001   HIS L  16 
 PHE   0.012   0.001   PHE R 100 
 TYR   0.010   0.001   TYR R 387 
 ARG   0.000   0.000   ARG R 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04473 (  181)
  hydrogen bonds       : angle       4.28602 (  537)
  SS BOND              : bond        0.00381 (    4)
  SS BOND              : angle       0.92039 (    8)
  covalent geometry    : bond        0.00320 ( 2376)
  covalent geometry    : angle       0.63277 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 54
  time to evaluate  : 0.270 
Fit side-chains
REVERT: R  236 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7144 (tp30)
REVERT: R  266 MET cc_start: 0.7366 (tpp) cc_final: 0.7037 (mmm)
  outliers start: 24
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0959
  time to fit residues: 9.2441
Evaluate side-chains
  66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  362 SER
Chi-restraints excluded: chain R residue  386 LEU
Chi-restraints excluded: chain L residue   15 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 378 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.202610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.189788 restraints weight = 3071.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.193771 restraints weight = 1583.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.196434 restraints weight = 933.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2380  Z= 0.141
  Angle     :  0.637  10.273   3253  Z= 0.320
  Chirality :  0.041   0.202    402
  Planarity :  0.006   0.103    388
  Dihedral  :  5.022  49.713    319
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 25.00 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.48), residues: 293
  helix:  1.59 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.35 (0.63), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  21 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.011   0.001   PHE R 100 
 TYR   0.009   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04336 (  181)
  hydrogen bonds       : angle       4.20069 (  537)
  SS BOND              : bond        0.00373 (    4)
  SS BOND              : angle       1.28157 (    8)
  covalent geometry    : bond        0.00320 ( 2376)
  covalent geometry    : angle       0.63444 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.278 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7757 (mp)
REVERT: R  266 MET cc_start: 0.7274 (tpp) cc_final: 0.6981 (mmm)
  outliers start: 20
  outliers final: 17
  residues processed: 72
  average time/residue: 0.0853
  time to fit residues: 8.0211
Evaluate side-chains
  66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  225 ILE
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Chi-restraints excluded: chain L residue   19 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.198839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.186973 restraints weight = 3015.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.190941 restraints weight = 1508.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.193374 restraints weight = 865.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2380  Z= 0.150
  Angle     :  0.668  10.873   3253  Z= 0.336
  Chirality :  0.042   0.205    402
  Planarity :  0.006   0.100    388
  Dihedral  :  5.090  50.840    319
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 26.21 %
    Favored  : 65.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.48), residues: 293
  helix:  1.57 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.28 (0.64), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP R 206 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.010   0.001   PHE R 100 
 TYR   0.017   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04388 (  181)
  hydrogen bonds       : angle       4.22443 (  537)
  SS BOND              : bond        0.00458 (    4)
  SS BOND              : angle       1.79692 (    8)
  covalent geometry    : bond        0.00349 ( 2376)
  covalent geometry    : angle       0.66320 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.286 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7744 (mp)
REVERT: R  266 MET cc_start: 0.7264 (tpp) cc_final: 0.6977 (mmm)
  outliers start: 21
  outliers final: 18
  residues processed: 69
  average time/residue: 0.0807
  time to fit residues: 7.4716
Evaluate side-chains
  69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  205 SER
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  225 ILE
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  330 LEU
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0870
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 373 ASN
** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.200382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.189068 restraints weight = 2999.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.192958 restraints weight = 1529.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.195270 restraints weight = 878.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2380  Z= 0.142
  Angle     :  0.710  10.110   3253  Z= 0.357
  Chirality :  0.043   0.203    402
  Planarity :  0.006   0.098    388
  Dihedral  :  5.231  51.182    319
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers : 10.89 %
    Allowed  : 22.58 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.48), residues: 293
  helix:  1.53 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.29 (0.64), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.010   0.001   PHE R 100 
 TYR   0.016   0.001   TYR R 387 
 ARG   0.000   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04292 (  181)
  hydrogen bonds       : angle       4.39489 (  537)
  SS BOND              : bond        0.00692 (    4)
  SS BOND              : angle       1.46117 (    8)
  covalent geometry    : bond        0.00322 ( 2376)
  covalent geometry    : angle       0.70680 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 54
  time to evaluate  : 0.307 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7712 (mp)
REVERT: R  266 MET cc_start: 0.7272 (tpp) cc_final: 0.6966 (mmm)
  outliers start: 27
  outliers final: 21
  residues processed: 76
  average time/residue: 0.0966
  time to fit residues: 9.8366
Evaluate side-chains
  72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 50
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  205 SER
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  225 ILE
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  362 SER
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Chi-restraints excluded: chain L residue   15 CYS
Chi-restraints excluded: chain L residue   19 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 373 ASN
** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.199417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.187730 restraints weight = 3110.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.191420 restraints weight = 1580.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.193830 restraints weight = 922.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2380  Z= 0.156
  Angle     :  0.721  10.209   3253  Z= 0.362
  Chirality :  0.043   0.205    402
  Planarity :  0.006   0.098    388
  Dihedral  :  5.376  52.656    319
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 25.81 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.49), residues: 293
  helix:  1.50 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.17 (0.67), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.012   0.001   PHE R 100 
 TYR   0.016   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04416 (  181)
  hydrogen bonds       : angle       4.36965 (  537)
  SS BOND              : bond        0.00715 (    4)
  SS BOND              : angle       1.84640 (    8)
  covalent geometry    : bond        0.00361 ( 2376)
  covalent geometry    : angle       0.71605 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.288 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7740 (mp)
REVERT: R  266 MET cc_start: 0.7325 (tpp) cc_final: 0.7036 (mmm)
  outliers start: 20
  outliers final: 17
  residues processed: 68
  average time/residue: 0.0870
  time to fit residues: 7.7790
Evaluate side-chains
  66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  205 SER
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  225 ILE
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Chi-restraints excluded: chain L residue   15 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R 137 ASN
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.201575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.189476 restraints weight = 3119.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.193386 restraints weight = 1585.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.195709 restraints weight = 921.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2380  Z= 0.142
  Angle     :  0.704   9.982   3253  Z= 0.354
  Chirality :  0.043   0.208    402
  Planarity :  0.006   0.098    388
  Dihedral  :  5.350  52.848    319
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  8.87 %
    Allowed  : 25.40 %
    Favored  : 65.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.49), residues: 293
  helix:  1.56 (0.33), residues: 230
  sheet: -4.30 (0.87), residues: 12
  loop : -2.89 (0.78), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.012   0.001   PHE R 240 
 TYR   0.019   0.001   TYR R 387 
 ARG   0.002   0.000   ARG R 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04406 (  181)
  hydrogen bonds       : angle       4.37122 (  537)
  SS BOND              : bond        0.00598 (    4)
  SS BOND              : angle       1.50548 (    8)
  covalent geometry    : bond        0.00319 ( 2376)
  covalent geometry    : angle       0.70067 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 46
  time to evaluate  : 0.282 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7703 (mp)
REVERT: R  266 MET cc_start: 0.7293 (tpp) cc_final: 0.7019 (mmm)
  outliers start: 22
  outliers final: 18
  residues processed: 64
  average time/residue: 0.0859
  time to fit residues: 7.2836
Evaluate side-chains
  64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  205 SER
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  225 ILE
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  330 LEU
Chi-restraints excluded: chain R residue  362 SER
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.1980
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.205454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.193951 restraints weight = 2948.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.197552 restraints weight = 1495.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.200014 restraints weight = 876.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2380  Z= 0.132
  Angle     :  0.688   9.363   3253  Z= 0.345
  Chirality :  0.042   0.207    402
  Planarity :  0.006   0.095    388
  Dihedral  :  5.218  52.661    319
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 27.82 %
    Favored  : 64.92 %
  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:  1.05 (0.50), residues: 293
  helix:  1.68 (0.33), residues: 230
  sheet: -4.07 (0.96), residues: 12
  loop : -2.69 (0.83), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 167 
 HIS   0.002   0.001   HIS L  16 
 PHE   0.011   0.001   PHE R 100 
 TYR   0.019   0.001   TYR R 387 
 ARG   0.002   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  181)
  hydrogen bonds       : angle       4.33496 (  537)
  SS BOND              : bond        0.00516 (    4)
  SS BOND              : angle       1.34386 (    8)
  covalent geometry    : bond        0.00289 ( 2376)
  covalent geometry    : angle       0.68513 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 0.252 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7652 (mp)
REVERT: R  268 PHE cc_start: 0.8323 (t80) cc_final: 0.7197 (t80)
  outliers start: 18
  outliers final: 16
  residues processed: 63
  average time/residue: 0.0764
  time to fit residues: 6.5174
Evaluate side-chains
  64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  205 SER
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  225 ILE
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  362 SER
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Chi-restraints excluded: chain R residue  388 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0770
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0770
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.207804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.195566 restraints weight = 3008.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.199310 restraints weight = 1535.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.201937 restraints weight = 905.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2380  Z= 0.133
  Angle     :  0.687   9.630   3253  Z= 0.341
  Chirality :  0.042   0.207    402
  Planarity :  0.006   0.095    388
  Dihedral  :  5.238  53.855    319
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 28.63 %
    Favored  : 64.52 %
  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:  1.05 (0.49), residues: 293
  helix:  1.66 (0.33), residues: 230
  sheet: -3.95 (1.05), residues: 12
  loop : -2.61 (0.85), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 167 
 HIS   0.002   0.001   HIS L  16 
 PHE   0.012   0.001   PHE R 100 
 TYR   0.019   0.001   TYR R 387 
 ARG   0.000   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  181)
  hydrogen bonds       : angle       4.30557 (  537)
  SS BOND              : bond        0.00543 (    4)
  SS BOND              : angle       1.26121 (    8)
  covalent geometry    : bond        0.00296 ( 2376)
  covalent geometry    : angle       0.68528 ( 3245)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.279 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7542 (mp)
REVERT: R  268 PHE cc_start: 0.8333 (t80) cc_final: 0.7175 (t80)
  outliers start: 17
  outliers final: 16
  residues processed: 61
  average time/residue: 0.0785
  time to fit residues: 6.4563
Evaluate side-chains
  66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  139 LEU
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  205 SER
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  225 ILE
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  362 SER
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Chi-restraints excluded: chain R residue  388 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 373 ASN
** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.204470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.192523 restraints weight = 2932.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.196398 restraints weight = 1503.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.198697 restraints weight = 872.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2380  Z= 0.137
  Angle     :  0.695   9.619   3253  Z= 0.346
  Chirality :  0.042   0.209    402
  Planarity :  0.006   0.094    388
  Dihedral  :  5.242  54.285    319
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 28.63 %
    Favored  : 64.11 %
  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:  1.04 (0.49), residues: 293
  helix:  1.65 (0.33), residues: 230
  sheet: -3.91 (1.09), residues: 12
  loop : -2.60 (0.84), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.012   0.001   PHE R 100 
 TYR   0.019   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  181)
  hydrogen bonds       : angle       4.28951 (  537)
  SS BOND              : bond        0.00542 (    4)
  SS BOND              : angle       1.26906 (    8)
  covalent geometry    : bond        0.00307 ( 2376)
  covalent geometry    : angle       0.69328 ( 3245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1169.63 seconds
wall clock time: 21 minutes 9.41 seconds (1269.41 seconds total)