Starting phenix.real_space_refine
on Fri May  9 13:35:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggl_40012/05_2025/8ggl_40012.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggl_40012/05_2025/8ggl_40012.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggl_40012/05_2025/8ggl_40012.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggl_40012/05_2025/8ggl_40012.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggl_40012/05_2025/8ggl_40012.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggl_40012/05_2025/8ggl_40012.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.030
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      16      5.16       5
     C    1436      2.51       5
     N     340      2.21       5
     O     359      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 2151
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2135
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 155
          Unresolved non-hydrogen angles: 191
          Unresolved non-hydrogen dihedrals: 130
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 104
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 2.61, per 1000 atoms: 1.21
  Number of scatterers: 2151
  At special positions: 0
  Unit cell: (56.4005, 82.4315, 61.6067, 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      16     16.00
     O     359      8.00
     N     340      7.00
     C    1436      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.59
  Conformation dependent library (CDL) restraints added in 274.0 milliseconds
  

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  544

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 0 sheets defined
      87.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 61
      removed outlier: 3.754A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 4.252A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.736A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 148 through 171
      removed outlier: 4.142A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE R 153 " --> pdb=" O   LYS R 149 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE R 154 " --> pdb=" O   ALA R 150 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.637A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 281
      removed outlier: 3.936A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 287
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 3.661A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 315
      removed outlier: 3.549A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 320
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 341

    161 hydrogen bonds defined for protein.
    477 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: 0.58

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 362
        1.33 -     1.45: 606
        1.45 -     1.57: 1215
        1.57 -     1.69: 0
        1.69 -     1.82: 22
  Bond restraints: 2205
  Sorted by residual:
  bond pdb=" C   MET R  36 "
       pdb=" N   GLY R  37 "
    ideal  model  delta    sigma   weight residual
    1.334  1.298  0.036 1.21e-02 6.83e+03 8.61e+00
  bond pdb=" CA  MET R  36 "
       pdb=" C   MET R  36 "
    ideal  model  delta    sigma   weight residual
    1.522  1.482  0.040 1.39e-02 5.18e+03 8.32e+00
  bond pdb=" CA  MET R  36 "
       pdb=" CB  MET R  36 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.044 1.68e-02 3.54e+03 6.88e+00
  bond pdb=" CA  VAL R  33 "
       pdb=" CB  VAL R  33 "
    ideal  model  delta    sigma   weight residual
    1.540  1.505  0.036 1.36e-02 5.41e+03 6.83e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.447 -0.050 2.00e-02 2.50e+03 6.27e+00
  ... (remaining 2200 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 2960
        1.69 -     3.39: 45
        3.39 -     5.08: 12
        5.08 -     6.78: 4
        6.78 -     8.47: 1
  Bond angle restraints: 3022
  Sorted by residual:
  angle pdb=" N   GLY R  35 "
        pdb=" CA  GLY R  35 "
        pdb=" C   GLY R  35 "
      ideal   model   delta    sigma   weight residual
     112.73  121.20   -8.47 1.20e+00 6.94e-01 4.99e+01
  angle pdb=" C   VAL R  34 "
        pdb=" CA  VAL R  34 "
        pdb=" CB  VAL R  34 "
      ideal   model   delta    sigma   weight residual
     112.14  105.60    6.54 1.35e+00 5.49e-01 2.35e+01
  angle pdb=" CA  GLY R  35 "
        pdb=" C   GLY R  35 "
        pdb=" O   GLY R  35 "
      ideal   model   delta    sigma   weight residual
     120.75  116.78    3.97 1.03e+00 9.43e-01 1.49e+01
  angle pdb=" CA  GLY R  35 "
        pdb=" C   GLY R  35 "
        pdb=" N   MET R  36 "
      ideal   model   delta    sigma   weight residual
     117.04  120.67   -3.63 9.90e-01 1.02e+00 1.34e+01
  angle pdb=" N   MET R  36 "
        pdb=" CA  MET R  36 "
        pdb=" C   MET R  36 "
      ideal   model   delta    sigma   weight residual
     112.89  108.92    3.97 1.24e+00 6.50e-01 1.02e+01
  ... (remaining 3017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.10: 1079
       11.10 -    22.21: 116
       22.21 -    33.31: 45
       33.31 -    44.41: 15
       44.41 -    55.52: 5
  Dihedral angle restraints: 1260
    sinusoidal: 424
      harmonic: 836
  Sorted by residual:
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.43  -17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CB  MET R 171 "
           pdb=" CG  MET R 171 "
           pdb=" SD  MET R 171 "
           pdb=" CE  MET R 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  127.53   52.47     3      1.50e+01 4.44e-03 9.12e+00
  dihedral pdb=" CG  ARG R 328 "
           pdb=" CD  ARG R 328 "
           pdb=" NE  ARG R 328 "
           pdb=" CZ  ARG R 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -140.45  -39.55     2      1.50e+01 4.44e-03 8.65e+00
  ... (remaining 1257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 219
       0.029 -    0.059: 97
       0.059 -    0.088: 38
       0.088 -    0.117: 19
       0.117 -    0.146: 1
  Chirality restraints: 374
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CA  VAL R  33 "
            pdb=" N   VAL R  33 "
            pdb=" C   VAL R  33 "
            pdb=" CB  VAL R  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.14e-01
  chirality pdb=" CA  VAL R  34 "
            pdb=" N   VAL R  34 "
            pdb=" C   VAL R  34 "
            pdb=" CB  VAL R  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.09e-01
  ... (remaining 371 not shown)

  Planarity restraints: 360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R  32 "   -0.017 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   TRP R  32 "    0.058 2.00e-02 2.50e+03
        pdb=" O   TRP R  32 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   VAL R  33 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  34 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.57e+00
        pdb=" C   VAL R  34 "    0.033 2.00e-02 2.50e+03
        pdb=" O   VAL R  34 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY R  35 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.83e+00
        pdb=" N   PRO R 211 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.024 5.00e-02 4.00e+02
  ... (remaining 357 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 652
        2.83 -     3.35: 2124
        3.35 -     3.86: 3356
        3.86 -     4.38: 3610
        4.38 -     4.90: 6603
  Nonbonded interactions: 16345
  Sorted by model distance:
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAK G1I R 501 "
     model   vdw
     2.482 3.040
  nonbonded pdb=" O   ARG R 175 "
            pdb=" ND2 ASN R 196 "
     model   vdw
     2.589 3.120
  nonbonded pdb=" N   MET R  36 "
            pdb=" N   GLY R  37 "
     model   vdw
     2.602 2.560
  ... (remaining 16340 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.040
  Process input model:                     11.590
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   2206  Z= 0.266
  Angle     :  0.619   8.473   3024  Z= 0.371
  Chirality :  0.041   0.146    374
  Planarity :  0.004   0.042    360
  Dihedral  : 12.383  55.517    713
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.50), residues: 278
  helix:  1.49 (0.36), residues: 214
  sheet:  None (None), residues: 0
  loop : -2.07 (0.64), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.008   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15324 (  161)
  hydrogen bonds       : angle       5.46665 (  477)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       1.30885 (    2)
  covalent geometry    : bond        0.00494 ( 2205)
  covalent geometry    : angle       0.61794 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.231 
Fit side-chains
REVERT: R  161 SER cc_start: 0.8768 (m) cc_final: 0.8466 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2420
  time to fit residues: 6.3570
Evaluate side-chains
  20 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   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 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.100619 restraints weight = 2864.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.52
r_work: 0.2971 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.0712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2206  Z= 0.157
  Angle     :  0.492   5.397   3024  Z= 0.272
  Chirality :  0.039   0.103    374
  Planarity :  0.004   0.045    360
  Dihedral  :  4.386  18.285    313
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  5.16 %
    Favored  : 92.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.27 (0.50), residues: 278
  helix:  1.64 (0.35), residues: 215
  sheet:  None (None), residues: 0
  loop : -2.01 (0.63), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06839 (  161)
  hydrogen bonds       : angle       4.28170 (  477)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       1.09913 (    2)
  covalent geometry    : bond        0.00357 ( 2205)
  covalent geometry    : angle       0.49154 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.240 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 24
  average time/residue: 0.2239
  time to fit residues: 6.1917
Evaluate side-chains
  23 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0870
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.6358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.114849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.100831 restraints weight = 2815.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.49
r_work: 0.2972 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2206  Z= 0.146
  Angle     :  0.469   5.339   3024  Z= 0.259
  Chirality :  0.038   0.103    374
  Planarity :  0.003   0.042    360
  Dihedral  :  4.303  18.439    313
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  :  6.57 %
    Favored  : 89.67 %
  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:  1.60 (0.49), residues: 278
  helix:  2.00 (0.36), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.75 (0.60), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06554 (  161)
  hydrogen bonds       : angle       4.13425 (  477)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       1.09753 (    2)
  covalent geometry    : bond        0.00326 ( 2205)
  covalent geometry    : angle       0.46792 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.242 
Fit side-chains
REVERT: R  296 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.8487 (p-80)
  outliers start: 8
  outliers final: 7
  residues processed: 26
  average time/residue: 0.2236
  time to fit residues: 6.7227
Evaluate side-chains
  27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.112357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.098425 restraints weight = 2810.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.48
r_work: 0.2934 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2206  Z= 0.171
  Angle     :  0.494   5.424   3024  Z= 0.272
  Chirality :  0.039   0.108    374
  Planarity :  0.004   0.042    360
  Dihedral  :  4.402  18.930    313
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  :  8.92 %
    Favored  : 86.85 %
  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:  1.53 (0.49), residues: 278
  helix:  1.94 (0.35), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.69 (0.60), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07144 (  161)
  hydrogen bonds       : angle       4.15972 (  477)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       1.10160 (    2)
  covalent geometry    : bond        0.00402 ( 2205)
  covalent geometry    : angle       0.49325 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 20
  time to evaluate  : 0.246 
Fit side-chains
REVERT: R  148 ASN cc_start: 0.8797 (t0) cc_final: 0.8569 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 27
  average time/residue: 0.2124
  time to fit residues: 6.6222
Evaluate side-chains
  27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.113253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.099259 restraints weight = 2880.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.51
r_work: 0.2946 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2206  Z= 0.153
  Angle     :  0.472   5.345   3024  Z= 0.260
  Chirality :  0.039   0.105    374
  Planarity :  0.003   0.038    360
  Dihedral  :  4.309  18.939    313
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 10.80 %
    Favored  : 84.98 %
  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:  1.67 (0.49), residues: 278
  helix:  2.02 (0.36), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.58 (0.62), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06731 (  161)
  hydrogen bonds       : angle       4.08136 (  477)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       1.03913 (    2)
  covalent geometry    : bond        0.00347 ( 2205)
  covalent geometry    : angle       0.47139 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 18
  time to evaluate  : 0.237 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 26
  average time/residue: 0.1936
  time to fit residues: 5.8774
Evaluate side-chains
  26 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 18
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.111843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.098013 restraints weight = 2855.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.48
r_work: 0.2930 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2206  Z= 0.168
  Angle     :  0.489   5.402   3024  Z= 0.269
  Chirality :  0.040   0.175    374
  Planarity :  0.003   0.039    360
  Dihedral  :  4.377  18.972    313
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 11.27 %
    Favored  : 84.51 %
  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:  1.66 (0.49), residues: 278
  helix:  1.99 (0.35), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.51 (0.64), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07069 (  161)
  hydrogen bonds       : angle       4.11007 (  477)
  SS BOND              : bond        0.00154 (    1)
  SS BOND              : angle       1.06720 (    2)
  covalent geometry    : bond        0.00395 ( 2205)
  covalent geometry    : angle       0.48865 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 19
  time to evaluate  : 0.228 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 26
  average time/residue: 0.1892
  time to fit residues: 5.7754
Evaluate side-chains
  27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.114264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.100332 restraints weight = 2851.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.49
r_work: 0.2963 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2206  Z= 0.139
  Angle     :  0.461   5.297   3024  Z= 0.253
  Chirality :  0.039   0.142    374
  Planarity :  0.003   0.036    360
  Dihedral  :  4.206  18.868    313
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 12.21 %
    Favored  : 84.51 %
  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:  1.90 (0.50), residues: 278
  helix:  2.19 (0.36), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.48 (0.64), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R 217 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06284 (  161)
  hydrogen bonds       : angle       3.99080 (  477)
  SS BOND              : bond        0.00144 (    1)
  SS BOND              : angle       1.11084 (    2)
  covalent geometry    : bond        0.00308 ( 2205)
  covalent geometry    : angle       0.46030 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: R  161 SER cc_start: 0.8657 (m) cc_final: 0.8448 (m)
  outliers start: 7
  outliers final: 7
  residues processed: 26
  average time/residue: 0.1872
  time to fit residues: 5.7065
Evaluate side-chains
  28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.114203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.100169 restraints weight = 2919.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 1.52
r_work: 0.2963 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2206  Z= 0.136
  Angle     :  0.456   5.311   3024  Z= 0.250
  Chirality :  0.038   0.126    374
  Planarity :  0.003   0.035    360
  Dihedral  :  4.177  18.798    313
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.21 %
    Favored  : 84.04 %
  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:  1.98 (0.50), residues: 278
  helix:  2.25 (0.36), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.49 (0.63), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.007   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06207 (  161)
  hydrogen bonds       : angle       3.98249 (  477)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       1.02889 (    2)
  covalent geometry    : bond        0.00300 ( 2205)
  covalent geometry    : angle       0.45489 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: R  161 SER cc_start: 0.8677 (m) cc_final: 0.8474 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 27
  average time/residue: 0.1883
  time to fit residues: 5.9720
Evaluate side-chains
  29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.112748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.098821 restraints weight = 2850.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.50
r_work: 0.2947 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
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   0.026   2206  Z= 0.154
  Angle     :  0.475   5.368   3024  Z= 0.260
  Chirality :  0.039   0.122    374
  Planarity :  0.003   0.035    360
  Dihedral  :  4.260  18.957    313
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.21 %
    Favored  : 84.04 %
  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:  1.80 (0.50), residues: 278
  helix:  2.00 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -1.44 (0.66), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06667 (  161)
  hydrogen bonds       : angle       4.02615 (  477)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       1.05756 (    2)
  covalent geometry    : bond        0.00355 ( 2205)
  covalent geometry    : angle       0.47397 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: R  161 SER cc_start: 0.8691 (m) cc_final: 0.8488 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 28
  average time/residue: 0.1796
  time to fit residues: 5.9135
Evaluate side-chains
  29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.112338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.098522 restraints weight = 2844.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.48
r_work: 0.2936 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2206  Z= 0.159
  Angle     :  0.483   5.378   3024  Z= 0.265
  Chirality :  0.039   0.120    374
  Planarity :  0.003   0.035    360
  Dihedral  :  4.296  19.016    313
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.21 %
    Favored  : 84.04 %
  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:  1.75 (0.49), residues: 278
  helix:  1.96 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -1.46 (0.66), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06823 (  161)
  hydrogen bonds       : angle       4.06667 (  477)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       1.05257 (    2)
  covalent geometry    : bond        0.00371 ( 2205)
  covalent geometry    : angle       0.48200 ( 3022)

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

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

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  556 Ramachandran restraints generated.
    278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.259 
Fit side-chains
REVERT: R  161 SER cc_start: 0.8675 (m) cc_final: 0.8473 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 27
  average time/residue: 0.1900
  time to fit residues: 6.0137
Evaluate side-chains
  29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.112564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.098648 restraints weight = 2857.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 1.51
r_work: 0.2943 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2206  Z= 0.154
  Angle     :  0.477   5.362   3024  Z= 0.262
  Chirality :  0.039   0.116    374
  Planarity :  0.003   0.035    360
  Dihedral  :  4.267  18.957    313
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.21 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.49), residues: 278
  helix:  1.98 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -1.48 (0.66), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06692 (  161)
  hydrogen bonds       : angle       4.04876 (  477)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       1.05413 (    2)
  covalent geometry    : bond        0.00355 ( 2205)
  covalent geometry    : angle       0.47593 ( 3022)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1551.34 seconds
wall clock time: 27 minutes 28.24 seconds (1648.24 seconds total)