Starting phenix.real_space_refine
on Wed Sep 17 03:00:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zrt_60404/09_2025/8zrt_60404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zrt_60404/09_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_60404/09_2025/8zrt_60404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zrt_60404/09_2025/8zrt_60404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zrt_60404/09_2025/8zrt_60404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zrt_60404/09_2025/8zrt_60404.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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, 'GLU:plan': 4, 'TYR:plan': 3, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1}
          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: 0.88, per 1000 atoms: 0.38
  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: 0.21
  Conformation dependent library (CDL) restraints added in 90.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.07
  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: 0.46

  Time building geometry restraints manager: 0.28 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:             0.760
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.370
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.850
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (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
 ARG   0.004   0.001   ARG R 357 
 TYR   0.008   0.001   TYR R 269 
 PHE   0.013   0.001   PHE R 100 
 TRP   0.007   0.001   TRP R 276 
 HIS   0.002   0.001   HIS R 258 

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

*********************** 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  : 0.092 
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: 0.0419
  time to fit residues: 3.0038
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  : 0.091 
-------------------------------------------------------------------------------
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 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0970
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 = 0.202457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.190174 restraints weight = 3071.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.193927 restraints weight = 1617.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.196469 restraints weight = 962.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.198074 restraints weight = 615.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.199061 restraints weight = 419.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.0871

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= 0.147
  Angle     :  0.642  11.086   3253  Z= 0.323
  Chirality :  0.041   0.208    402
  Planarity :  0.007   0.122    388
  Dihedral  :  4.925  47.671    319
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.48), residues: 293
  helix:  1.41 (0.33), residues: 229
  sheet:  None (None), residues: 0
  loop : -3.26 (0.63), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 357 
 TYR   0.007   0.001   TYR R 281 
 PHE   0.011   0.001   PHE R 397 
 TRP   0.006   0.001   TRP L  21 
 HIS   0.003   0.001   HIS L  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 2376)
  covalent geometry    : angle       0.64115 ( 3245)
  SS BOND              : bond        0.00298 (    4)
  SS BOND              : angle       1.00176 (    8)
  hydrogen bonds       : bond        0.04608 (  181)
  hydrogen bonds       : angle       4.40680 (  537)

*********************** 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  : 0.086 
Fit side-chains
REVERT: R  236 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7034 (tp30)
REVERT: R  266 MET cc_start: 0.7297 (tpp) cc_final: 0.6956 (mmm)
  outliers start: 14
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0420
  time to fit residues: 3.5769
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  : 0.086 
-------------------------------------------------------------------------------
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 27 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0010
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 = 0.4349 r_free = 0.4349 target = 0.203941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.191054 restraints weight = 3116.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.194908 restraints weight = 1573.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.197605 restraints weight = 928.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.199279 restraints weight = 593.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.200456 restraints weight = 405.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2380  Z= 0.133
  Angle     :  0.622  10.414   3253  Z= 0.313
  Chirality :  0.041   0.201    402
  Planarity :  0.007   0.106    388
  Dihedral  :  4.898  47.441    319
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  8.87 %
    Allowed  : 25.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.48), residues: 293
  helix:  1.54 (0.33), residues: 229
  sheet:  None (None), residues: 0
  loop : -3.31 (0.63), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 392 
 TYR   0.009   0.001   TYR R 387 
 PHE   0.012   0.001   PHE R 100 
 TRP   0.005   0.001   TRP R 276 
 HIS   0.003   0.001   HIS L  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2376)
  covalent geometry    : angle       0.62177 ( 3245)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       0.80028 (    8)
  hydrogen bonds       : bond        0.04357 (  181)
  hydrogen bonds       : angle       4.27063 (  537)

*********************** 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
  75 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 53
  time to evaluate  : 0.094 
Fit side-chains
REVERT: R  236 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7145 (tp30)
REVERT: R  266 MET cc_start: 0.7280 (tpp) cc_final: 0.6950 (mmm)
  outliers start: 22
  outliers final: 13
  residues processed: 72
  average time/residue: 0.0469
  time to fit residues: 4.2044
Evaluate side-chains
  64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
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  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  234 VAL
Chi-restraints excluded: chain R residue  258 HIS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 2 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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.199792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.187859 restraints weight = 3041.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.191707 restraints weight = 1556.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.194116 restraints weight = 907.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.195581 restraints weight = 577.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.196771 restraints weight = 402.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.1311

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     :  0.643  10.801   3253  Z= 0.322
  Chirality :  0.041   0.205    402
  Planarity :  0.006   0.102    388
  Dihedral  :  4.926  48.594    319
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 25.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.48), residues: 293
  helix:  1.59 (0.33), residues: 229
  sheet:  None (None), residues: 0
  loop : -3.32 (0.64), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 357 
 TYR   0.009   0.001   TYR R 387 
 PHE   0.009   0.001   PHE R 100 
 TRP   0.006   0.001   TRP R 336 
 HIS   0.002   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 2376)
  covalent geometry    : angle       0.64128 ( 3245)
  SS BOND              : bond        0.00389 (    4)
  SS BOND              : angle       1.21924 (    8)
  hydrogen bonds       : bond        0.04349 (  181)
  hydrogen bonds       : angle       4.19809 (  537)

*********************** 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
  75 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.146 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7750 (mp)
REVERT: R  266 MET cc_start: 0.7284 (tpp) cc_final: 0.6950 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 73
  average time/residue: 0.0356
  time to fit residues: 3.4879
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  : 0.106 
-------------------------------------------------------------------------------
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  379 SER
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 21 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4315 r_free = 0.4315 target = 0.198423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.186593 restraints weight = 2992.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.190490 restraints weight = 1512.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.192855 restraints weight = 868.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.194458 restraints weight = 555.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.195541 restraints weight = 370.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2380  Z= 0.154
  Angle     :  0.667  10.213   3253  Z= 0.334
  Chirality :  0.042   0.204    402
  Planarity :  0.006   0.099    388
  Dihedral  :  5.073  50.329    319
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  9.68 %
    Allowed  : 25.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.48), residues: 293
  helix:  1.53 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.25 (0.64), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 357 
 TYR   0.009   0.001   TYR R 387 
 PHE   0.011   0.001   PHE R 100 
 TRP   0.008   0.001   TRP R 206 
 HIS   0.002   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 2376)
  covalent geometry    : angle       0.66187 ( 3245)
  SS BOND              : bond        0.00554 (    4)
  SS BOND              : angle       1.82978 (    8)
  hydrogen bonds       : bond        0.04426 (  181)
  hydrogen bonds       : angle       4.24305 (  537)

*********************** 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: 24
    poor density    : 50
  time to evaluate  : 0.054 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7651 (mp)
REVERT: R  266 MET cc_start: 0.7263 (tpp) cc_final: 0.6951 (mmm)
  outliers start: 24
  outliers final: 20
  residues processed: 71
  average time/residue: 0.0288
  time to fit residues: 2.7853
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  : 0.092 
-------------------------------------------------------------------------------
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  362 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4343 r_free = 0.4343 target = 0.202760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.190734 restraints weight = 3083.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.194728 restraints weight = 1604.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.197174 restraints weight = 934.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.198566 restraints weight = 589.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.199694 restraints weight = 408.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.1625

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= 0.153
  Angle     :  0.729  10.761   3253  Z= 0.368
  Chirality :  0.044   0.203    402
  Planarity :  0.006   0.098    388
  Dihedral  :  5.247  50.810    319
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  9.27 %
    Allowed  : 24.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.48), residues: 293
  helix:  1.49 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.26 (0.65), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 357 
 TYR   0.018   0.001   TYR R 387 
 PHE   0.010   0.001   PHE R 100 
 TRP   0.015   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 2376)
  covalent geometry    : angle       0.72405 ( 3245)
  SS BOND              : bond        0.00671 (    4)
  SS BOND              : angle       1.91310 (    8)
  hydrogen bonds       : bond        0.04451 (  181)
  hydrogen bonds       : angle       4.41237 (  537)

*********************** 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
  73 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 50
  time to evaluate  : 0.097 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7735 (mp)
REVERT: R  266 MET cc_start: 0.7276 (tpp) cc_final: 0.6973 (mmm)
  outliers start: 23
  outliers final: 19
  residues processed: 69
  average time/residue: 0.0341
  time to fit residues: 3.1456
Evaluate side-chains
  67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 28 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.2980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4345 r_free = 0.4345 target = 0.201754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.190286 restraints weight = 3124.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.194208 restraints weight = 1564.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.196601 restraints weight = 892.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.198025 restraints weight = 557.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.199107 restraints weight = 374.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.1699

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     :  0.703  10.477   3253  Z= 0.354
  Chirality :  0.042   0.206    402
  Planarity :  0.006   0.096    388
  Dihedral  :  5.261  51.278    319
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  8.87 %
    Allowed  : 25.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.48), residues: 293
  helix:  1.53 (0.33), residues: 230
  sheet:  None (None), residues: 0
  loop : -3.16 (0.66), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 357 
 TYR   0.017   0.001   TYR R 387 
 PHE   0.013   0.001   PHE R 100 
 TRP   0.016   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2376)
  covalent geometry    : angle       0.69991 ( 3245)
  SS BOND              : bond        0.00500 (    4)
  SS BOND              : angle       1.57219 (    8)
  hydrogen bonds       : bond        0.04313 (  181)
  hydrogen bonds       : angle       4.36171 (  537)

*********************** 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: 22
    poor density    : 53
  time to evaluate  : 0.087 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7690 (mp)
REVERT: R  266 MET cc_start: 0.7264 (tpp) cc_final: 0.6956 (mmm)
  outliers start: 22
  outliers final: 18
  residues processed: 71
  average time/residue: 0.0305
  time to fit residues: 2.9207
Evaluate side-chains
  67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
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  362 SER
Chi-restraints excluded: chain R residue  378 ASN
Chi-restraints excluded: chain R residue  386 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0670
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.4356 r_free = 0.4356 target = 0.202850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.191270 restraints weight = 2934.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.195059 restraints weight = 1516.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.197336 restraints weight = 881.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.198959 restraints weight = 564.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.199839 restraints weight = 381.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.1839

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= 0.138
  Angle     :  0.690  10.050   3253  Z= 0.348
  Chirality :  0.042   0.203    402
  Planarity :  0.006   0.097    388
  Dihedral  :  5.260  51.827    319
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 26.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.49), residues: 293
  helix:  1.58 (0.33), residues: 230
  sheet: -4.19 (0.89), residues: 12
  loop : -2.77 (0.80), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 357 
 TYR   0.018   0.001   TYR R 387 
 PHE   0.012   0.001   PHE R 100 
 TRP   0.015   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 2376)
  covalent geometry    : angle       0.68691 ( 3245)
  SS BOND              : bond        0.00510 (    4)
  SS BOND              : angle       1.45519 (    8)
  hydrogen bonds       : bond        0.04307 (  181)
  hydrogen bonds       : angle       4.36730 (  537)

*********************** 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: 19
    poor density    : 49
  time to evaluate  : 0.095 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7657 (mp)
REVERT: R  266 MET cc_start: 0.7258 (tpp) cc_final: 0.6947 (mmm)
  outliers start: 19
  outliers final: 17
  residues processed: 64
  average time/residue: 0.0284
  time to fit residues: 2.5247
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  : 0.087 
-------------------------------------------------------------------------------
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  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 13 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0370
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0570
   overall best weight:    0.4376

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.204945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.193250 restraints weight = 3040.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.196842 restraints weight = 1541.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.199340 restraints weight = 909.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.200803 restraints weight = 576.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.201904 restraints weight = 396.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.1996

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= 0.132
  Angle     :  0.677   9.515   3253  Z= 0.340
  Chirality :  0.042   0.209    402
  Planarity :  0.006   0.094    388
  Dihedral  :  5.208  52.458    319
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  8.87 %
    Allowed  : 26.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.49), residues: 293
  helix:  1.68 (0.33), residues: 230
  sheet: -3.98 (0.99), residues: 12
  loop : -2.67 (0.82), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 199 
 TYR   0.019   0.001   TYR R 387 
 PHE   0.014   0.001   PHE R 100 
 TRP   0.013   0.002   TRP R 167 
 HIS   0.002   0.001   HIS L  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 2376)
  covalent geometry    : angle       0.67497 ( 3245)
  SS BOND              : bond        0.00503 (    4)
  SS BOND              : angle       1.17208 (    8)
  hydrogen bonds       : bond        0.04096 (  181)
  hydrogen bonds       : angle       4.32777 (  537)

*********************** 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
  72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 50
  time to evaluate  : 0.086 
Fit side-chains
REVERT: R  225 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7577 (mp)
  outliers start: 22
  outliers final: 18
  residues processed: 67
  average time/residue: 0.0284
  time to fit residues: 2.6385
Evaluate side-chains
  68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
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  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 R residue  388 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4358 r_free = 0.4358 target = 0.203483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.191226 restraints weight = 3085.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.195185 restraints weight = 1592.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.197686 restraints weight = 924.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.199352 restraints weight = 583.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.200274 restraints weight = 391.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.2053

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     :  0.695   9.686   3253  Z= 0.350
  Chirality :  0.043   0.199    402
  Planarity :  0.006   0.095    388
  Dihedral  :  5.283  53.810    319
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 27.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.49), residues: 293
  helix:  1.66 (0.33), residues: 230
  sheet: -3.94 (1.03), residues: 12
  loop : -2.61 (0.85), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 357 
 TYR   0.019   0.002   TYR R 387 
 PHE   0.014   0.001   PHE R 100 
 TRP   0.015   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 2376)
  covalent geometry    : angle       0.69287 ( 3245)
  SS BOND              : bond        0.00604 (    4)
  SS BOND              : angle       1.36355 (    8)
  hydrogen bonds       : bond        0.04121 (  181)
  hydrogen bonds       : angle       4.32227 (  537)

********************** 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
  67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.095 
Fit side-chains
REVERT: R  206 TRP cc_start: 0.6551 (p90) cc_final: 0.6306 (p90)
REVERT: R  225 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7598 (mp)
REVERT: R  266 MET cc_start: 0.7302 (tpp) cc_final: 0.6986 (mmm)
REVERT: R  268 PHE cc_start: 0.8271 (t80) cc_final: 0.7141 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 62
  average time/residue: 0.0311
  time to fit residues: 2.6767
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  : 0.090 
-------------------------------------------------------------------------------
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4356 r_free = 0.4356 target = 0.203315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.191319 restraints weight = 3077.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.195010 restraints weight = 1567.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.197537 restraints weight = 923.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.199215 restraints weight = 582.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.200275 restraints weight = 392.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.2107

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= 0.141
  Angle     :  0.691  10.022   3253  Z= 0.347
  Chirality :  0.043   0.199    402
  Planarity :  0.006   0.093    388
  Dihedral  :  5.321  54.149    319
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.49), residues: 293
  helix:  1.68 (0.33), residues: 230
  sheet: -3.87 (1.07), residues: 12
  loop : -2.63 (0.85), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 357 
 TYR   0.021   0.002   TYR R 200 
 PHE   0.014   0.001   PHE R 100 
 TRP   0.014   0.002   TRP R 167 
 HIS   0.002   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 2376)
  covalent geometry    : angle       0.68881 ( 3245)
  SS BOND              : bond        0.00577 (    4)
  SS BOND              : angle       1.35237 (    8)
  hydrogen bonds       : bond        0.04147 (  181)
  hydrogen bonds       : angle       4.30263 (  537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 608.82 seconds
wall clock time: 11 minutes 5.39 seconds (665.39 seconds total)