Starting phenix.real_space_refine
on Fri May  9 14:06:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zrt_60404/05_2025/8zrt_60404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zrt_60404/05_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_60404/05_2025/8zrt_60404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zrt_60404/05_2025/8zrt_60404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zrt_60404/05_2025/8zrt_60404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zrt_60404/05_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-5687/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: 1.96, per 1000 atoms: 0.84
  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: 0.51
  Conformation dependent library (CDL) restraints added in 249.8 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: 0.28
  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: 0.59

  Time building geometry restraints manager: 0.63 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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.570
-------------------------------------------------------------------------------
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  : 0.260 
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: 0.0903
  time to fit residues: 6.3882
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  : 0.248 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.200765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.188640 restraints weight = 3083.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.192387 restraints weight = 1573.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.194843 restraints weight = 926.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.0914

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= 0.151
  Angle     :  0.647  11.171   3253  Z= 0.325
  Chirality :  0.041   0.209    402
  Planarity :  0.007   0.122    388
  Dihedral  :  4.953  47.948    319
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 26.61 %
    Favored  : 68.15 %
  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:  1.36 (0.33), residues: 229
  sheet:  None (None), residues: 0
  loop : -3.28 (0.63), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  21 
 HIS   0.002   0.001   HIS L  16 
 PHE   0.010   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        0.04631 (  181)
  hydrogen bonds       : angle       4.43496 (  537)
  SS BOND              : bond        0.00494 (    4)
  SS BOND              : angle       1.06295 (    8)
  covalent geometry    : bond        0.00336 ( 2376)
  covalent geometry    : angle       0.64535 ( 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
  69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.266 
Fit side-chains
REVERT: R  236 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7030 (tp30)
REVERT: R  266 MET cc_start: 0.7320 (tpp) cc_final: 0.6998 (mmm)
  outliers start: 13
  outliers final: 9
  residues processed: 66
  average time/residue: 0.1009
  time to fit residues: 8.3334
Evaluate side-chains
  61 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  386 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4316 r_free = 0.4316 target = 0.199969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.187593 restraints weight = 3076.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.191279 restraints weight = 1640.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.193792 restraints weight = 983.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2380  Z= 0.154
  Angle     :  0.645  10.772   3253  Z= 0.326
  Chirality :  0.042   0.209    402
  Planarity :  0.007   0.108    388
  Dihedral  :  5.078  49.616    319
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers : 10.48 %
    Allowed  : 24.19 %
    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:  0.64 (0.48), residues: 293
  helix:  1.43 (0.33), residues: 229
  sheet:  None (None), residues: 0
  loop : -3.45 (0.61), 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   0.013   0.001   PHE R 100 
 TYR   0.011   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04562 (  181)
  hydrogen bonds       : angle       4.31135 (  537)
  SS BOND              : bond        0.00501 (    4)
  SS BOND              : angle       1.01404 (    8)
  covalent geometry    : bond        0.00355 ( 2376)
  covalent geometry    : angle       0.64376 ( 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
  79 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 53
  time to evaluate  : 0.274 
Fit side-chains
REVERT: R  236 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7151 (tp30)
REVERT: R  266 MET cc_start: 0.7343 (tpp) cc_final: 0.7026 (mmm)
  outliers start: 26
  outliers final: 16
  residues processed: 76
  average time/residue: 0.1054
  time to fit residues: 10.0077
Evaluate side-chains
  70 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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  234 VAL
Chi-restraints excluded: chain R residue  256 LEU
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  379 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:    6.9990
   chunk 29 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.201938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.189801 restraints weight = 3061.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.193400 restraints weight = 1585.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.195908 restraints weight = 953.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.1374

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= 0.143
  Angle     :  0.645  10.375   3253  Z= 0.324
  Chirality :  0.041   0.203    402
  Planarity :  0.007   0.103    388
  Dihedral  :  5.044  49.889    319
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 25.81 %
    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:  0.84 (0.48), residues: 293
  helix:  1.55 (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 R 276 
 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 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04409 (  181)
  hydrogen bonds       : angle       4.21989 (  537)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       1.47802 (    8)
  covalent geometry    : bond        0.00323 ( 2376)
  covalent geometry    : angle       0.64144 ( 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
  77 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.290 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7791 (mp)
REVERT: R  266 MET cc_start: 0.7287 (tpp) cc_final: 0.6998 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 74
  average time/residue: 0.0872
  time to fit residues: 8.1890
Evaluate side-chains
  69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  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  379 SER
Chi-restraints excluded: chain R residue  386 LEU
Chi-restraints excluded: chain L residue   15 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   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 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 = 0.4333 r_free = 0.4333 target = 0.202016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.189772 restraints weight = 3103.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.193470 restraints weight = 1603.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.195755 restraints weight = 955.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2380  Z= 0.142
  Angle     :  0.648  10.850   3253  Z= 0.325
  Chirality :  0.041   0.206    402
  Planarity :  0.006   0.100    388
  Dihedral  :  5.056  50.736    319
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 27.02 %
    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:  0.88 (0.48), residues: 293
  helix:  1.58 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.33 (0.63), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   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 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04351 (  181)
  hydrogen bonds       : angle       4.18551 (  537)
  SS BOND              : bond        0.00400 (    4)
  SS BOND              : angle       1.22844 (    8)
  covalent geometry    : bond        0.00323 ( 2376)
  covalent geometry    : angle       0.64633 ( 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
  77 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.213 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7742 (mp)
REVERT: R  266 MET cc_start: 0.7264 (tpp) cc_final: 0.6994 (mmm)
  outliers start: 21
  outliers final: 19
  residues processed: 72
  average time/residue: 0.0933
  time to fit residues: 8.6829
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  : 0.270 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain L residue   19 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4316 r_free = 0.4316 target = 0.198696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.187182 restraints weight = 2901.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.190997 restraints weight = 1473.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.193421 restraints weight = 843.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2380  Z= 0.147
  Angle     :  0.663  10.255   3253  Z= 0.335
  Chirality :  0.042   0.203    402
  Planarity :  0.006   0.099    388
  Dihedral  :  5.114  51.787    319
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers : 10.48 %
    Allowed  : 25.40 %
    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:  0.84 (0.48), residues: 293
  helix:  1.53 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.26 (0.64), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 206 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.016   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        0.04360 (  181)
  hydrogen bonds       : angle       4.23229 (  537)
  SS BOND              : bond        0.00518 (    4)
  SS BOND              : angle       1.72563 (    8)
  covalent geometry    : bond        0.00343 ( 2376)
  covalent geometry    : angle       0.65812 ( 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
  78 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 0.264 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7739 (mp)
REVERT: R  266 MET cc_start: 0.7289 (tpp) cc_final: 0.7025 (mmm)
  outliers start: 26
  outliers final: 20
  residues processed: 73
  average time/residue: 0.0915
  time to fit residues: 8.5448
Evaluate side-chains
  69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4327 r_free = 0.4327 target = 0.199817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.187891 restraints weight = 3066.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.191710 restraints weight = 1533.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.194232 restraints weight = 890.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2380  Z= 0.150
  Angle     :  0.695  10.022   3253  Z= 0.348
  Chirality :  0.042   0.204    402
  Planarity :  0.006   0.098    388
  Dihedral  :  5.252  52.952    319
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  9.27 %
    Allowed  : 26.61 %
    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:  0.82 (0.48), residues: 293
  helix:  1.51 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.21 (0.66), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.010   0.001   PHE R 100 
 TYR   0.018   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  181)
  hydrogen bonds       : angle       4.30033 (  537)
  SS BOND              : bond        0.00399 (    4)
  SS BOND              : angle       2.50104 (    8)
  covalent geometry    : bond        0.00348 ( 2376)
  covalent geometry    : angle       0.68477 ( 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
  75 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.242 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7742 (mp)
REVERT: R  266 MET cc_start: 0.7304 (tpp) cc_final: 0.7041 (mmm)
  outliers start: 23
  outliers final: 21
  residues processed: 69
  average time/residue: 0.0919
  time to fit residues: 8.0272
Evaluate side-chains
  69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  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
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:    0.1980
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 0 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:
R 137 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.200567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.188448 restraints weight = 3072.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.192358 restraints weight = 1557.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.194912 restraints weight = 895.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.1924

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= 0.146
  Angle     :  0.687  10.178   3253  Z= 0.344
  Chirality :  0.042   0.204    402
  Planarity :  0.006   0.097    388
  Dihedral  :  5.236  53.579    319
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  9.68 %
    Allowed  : 26.61 %
    Favored  : 63.71 %
  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:  0.86 (0.48), residues: 293
  helix:  1.53 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.19 (0.66), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.009   0.001   PHE R 397 
 TYR   0.020   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  181)
  hydrogen bonds       : angle       4.27795 (  537)
  SS BOND              : bond        0.00344 (    4)
  SS BOND              : angle       2.17273 (    8)
  covalent geometry    : bond        0.00337 ( 2376)
  covalent geometry    : angle       0.67938 ( 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
  74 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 0.262 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7717 (mp)
REVERT: R  266 MET cc_start: 0.7284 (tpp) cc_final: 0.7022 (mmm)
REVERT: R  268 PHE cc_start: 0.8279 (t80) cc_final: 0.7171 (t80)
  outliers start: 24
  outliers final: 19
  residues processed: 69
  average time/residue: 0.0940
  time to fit residues: 8.2296
Evaluate side-chains
  66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  177 VAL
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  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=1.50
-------------------------------------------------------------------------------
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:    0.8980
   chunk 14 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0020
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 = 0.4341 r_free = 0.4341 target = 0.201642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.189750 restraints weight = 2922.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.193566 restraints weight = 1482.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.196090 restraints weight = 856.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.1929

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= 0.141
  Angle     :  0.682  10.024   3253  Z= 0.339
  Chirality :  0.041   0.199    402
  Planarity :  0.006   0.097    388
  Dihedral  :  5.218  53.864    319
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 28.23 %
    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:  0.92 (0.49), residues: 293
  helix:  1.56 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.10 (0.69), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.009   0.001   PHE R 397 
 TYR   0.019   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 343 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04313 (  181)
  hydrogen bonds       : angle       4.26035 (  537)
  SS BOND              : bond        0.00316 (    4)
  SS BOND              : angle       1.81074 (    8)
  covalent geometry    : bond        0.00319 ( 2376)
  covalent geometry    : angle       0.67673 ( 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
  70 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 51
  time to evaluate  : 0.270 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7710 (mp)
REVERT: R  266 MET cc_start: 0.7272 (tpp) cc_final: 0.7014 (mmm)
REVERT: R  268 PHE cc_start: 0.8288 (t80) cc_final: 0.7180 (t80)
  outliers start: 19
  outliers final: 17
  residues processed: 65
  average time/residue: 0.1016
  time to fit residues: 8.4040
Evaluate side-chains
  65 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  162 LEU
Chi-restraints excluded: chain R residue  177 VAL
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 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:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0030
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5390

-------------------------------------------------------------------------------
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 = 0.4351 r_free = 0.4351 target = 0.202905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.190770 restraints weight = 2969.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.194690 restraints weight = 1502.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.197181 restraints weight = 866.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.2095

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= 0.136
  Angle     :  0.674   9.860   3253  Z= 0.335
  Chirality :  0.041   0.195    402
  Planarity :  0.006   0.094    388
  Dihedral  :  5.187  54.355    319
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 28.23 %
    Favored  : 63.71 %
  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:  1.00 (0.49), residues: 293
  helix:  1.60 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.01 (0.70), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 167 
 HIS   0.002   0.001   HIS R 258 
 PHE   0.009   0.001   PHE R 397 
 TYR   0.020   0.001   TYR R 387 
 ARG   0.001   0.000   ARG R 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  181)
  hydrogen bonds       : angle       4.22847 (  537)
  SS BOND              : bond        0.00290 (    4)
  SS BOND              : angle       1.69835 (    8)
  covalent geometry    : bond        0.00304 ( 2376)
  covalent geometry    : angle       0.66938 ( 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
  74 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.257 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7598 (mp)
REVERT: R  268 PHE cc_start: 0.8351 (t80) cc_final: 0.7186 (t80)
  outliers start: 20
  outliers final: 18
  residues processed: 69
  average time/residue: 0.0963
  time to fit residues: 8.3890
Evaluate side-chains
  70 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 51
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  162 LEU
Chi-restraints excluded: chain R residue  177 VAL
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  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:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 23 optimal weight:    0.1980
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0570
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.204138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.192376 restraints weight = 2944.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.196060 restraints weight = 1471.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.198593 restraints weight = 855.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.2155

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     :  0.669   9.645   3253  Z= 0.332
  Chirality :  0.042   0.203    402
  Planarity :  0.006   0.095    388
  Dihedral  :  5.175  54.584    319
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 29.84 %
    Favored  : 62.90 %
  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:  1.03 (0.49), residues: 293
  helix:  1.62 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -2.96 (0.70), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   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   0.002   0.000   ARG R 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  181)
  hydrogen bonds       : angle       4.23365 (  537)
  SS BOND              : bond        0.00233 (    4)
  SS BOND              : angle       1.52091 (    8)
  covalent geometry    : bond        0.00296 ( 2376)
  covalent geometry    : angle       0.66528 ( 3245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1058.01 seconds
wall clock time: 19 minutes 15.58 seconds (1155.58 seconds total)