Starting phenix.real_space_refine
on Fri May  9 13:48:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggk_40011/05_2025/8ggk_40011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggk_40011/05_2025/8ggk_40011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggk_40011/05_2025/8ggk_40011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggk_40011/05_2025/8ggk_40011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggk_40011/05_2025/8ggk_40011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggk_40011/05_2025/8ggk_40011.cif"
  }
  resolution = 3.3
  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=   0.028
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    1479      2.51       5
     N     353      2.21       5
     O     370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2201
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 7, 'TRANS': 280}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 121
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 82
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 17
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 2.23, per 1000 atoms: 1.01
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.0036, 86.77, 62.4744, 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     370      8.00
     N     353      7.00
     C    1479      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: 0.44
  Conformation dependent library (CDL) restraints added in 285.9 milliseconds
  

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  552

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      87.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.680A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.553A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.516A  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: 3.768A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 148 through 166
      removed outlier: 3.687A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ILE R 154 " --> pdb=" O   ALA R 150 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
    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
    Processing helix  chain 'R' and resid 269 through 281
    Processing helix  chain 'R' and resid 282 through 287
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 3.545A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.691A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340

    166 hydrogen bonds defined for protein.
    498 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: 0.51

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 660
        1.35 -     1.46: 608
        1.46 -     1.58: 984
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 2274
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.39e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 2.00e-02 2.50e+03 4.70e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.436 -0.042 2.00e-02 2.50e+03 4.46e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 2.00e-02 2.50e+03 3.87e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.319  0.034 2.00e-02 2.50e+03 2.90e+00
  ... (remaining 2269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 2985
        1.11 -     2.22: 100
        2.22 -     3.33: 15
        3.33 -     4.44: 7
        4.44 -     5.55: 7
  Bond angle restraints: 3114
  Sorted by residual:
  angle pdb=" C   HIS R 241 "
        pdb=" N   VAL R 242 "
        pdb=" CA  VAL R 242 "
      ideal   model   delta    sigma   weight residual
     121.70  125.97   -4.27 1.80e+00 3.09e-01 5.64e+00
  angle pdb=" N   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" C   VAL R  87 "
      ideal   model   delta    sigma   weight residual
     108.88  112.82   -3.94 2.16e+00 2.14e-01 3.33e+00
  angle pdb=" N   SER R 207 "
        pdb=" CA  SER R 207 "
        pdb=" C   SER R 207 "
      ideal   model   delta    sigma   weight residual
     111.69  113.86   -2.17 1.23e+00 6.61e-01 3.11e+00
  angle pdb=" CAE G1I R 501 "
        pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
      ideal   model   delta    sigma   weight residual
     112.63  117.69   -5.06 3.00e+00 1.11e-01 2.84e+00
  angle pdb=" C   THR R  96 "
        pdb=" N   LYS R  97 "
        pdb=" CA  LYS R  97 "
      ideal   model   delta    sigma   weight residual
     124.31  127.11   -2.80 1.67e+00 3.59e-01 2.80e+00
  ... (remaining 3109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.74: 1081
       10.74 -    21.47: 139
       21.47 -    32.20: 55
       32.20 -    42.93: 23
       42.93 -    53.67: 5
  Dihedral angle restraints: 1303
    sinusoidal: 454
      harmonic: 849
  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 -159.29  -20.71     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  HIS R 178 "
           pdb=" C   HIS R 178 "
           pdb=" N   GLN R 179 "
           pdb=" CA  GLN R 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.07  -16.93     0      5.00e+00 4.00e-02 1.15e+01
  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  136.83   43.17     2      1.50e+01 4.44e-03 9.99e+00
  ... (remaining 1300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 214
       0.030 -    0.060: 117
       0.060 -    0.090: 36
       0.090 -    0.120: 14
       0.120 -    0.151: 1
  Chirality restraints: 382
  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 5.67e-01
  chirality pdb=" CA  LEU R 287 "
            pdb=" N   LEU R 287 "
            pdb=" C   LEU R 287 "
            pdb=" CB  LEU R 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.80e-01
  chirality pdb=" CA  ASN R 322 "
            pdb=" N   ASN R 322 "
            pdb=" C   ASN R 322 "
            pdb=" CB  ASN R 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.41    0.10 2.00e-01 2.50e+01 2.60e-01
  ... (remaining 379 not shown)

  Planarity restraints: 372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.014 5.00e-02 4.00e+02   2.05e-02 6.74e-01
        pdb=" N   PRO R 323 "   -0.035 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.013 5.00e-02 4.00e+02   1.97e-02 6.23e-01
        pdb=" N   PRO R 211 "   -0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.013 5.00e-02 4.00e+02   1.93e-02 5.95e-01
        pdb=" N   PRO R 168 "    0.033 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 369 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 512
        2.79 -     3.32: 2157
        3.32 -     3.84: 3513
        3.84 -     4.37: 3734
        4.37 -     4.90: 6864
  Nonbonded interactions: 16780
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OH  TYR R 174 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" N   HIS R 178 "
            pdb=" O   HIS R 178 "
     model   vdw
     2.641 2.496
  ... (remaining 16775 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:             1.430
  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:                    0.020
  Process input model:                     10.010
  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:2.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
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      :  0.004   0.051   2275  Z= 0.205
  Angle     :  0.550   5.548   3116  Z= 0.299
  Chirality :  0.040   0.151    382
  Planarity :  0.003   0.021    372
  Dihedral  : 12.874  53.666    748
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 (0.52), residues: 284
  helix:  2.00 (0.36), residues: 211
  sheet:  None (None), residues: 0
  loop : -1.34 (0.75), residues: 73

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   0.009   0.001   PHE R 104 
 TYR   0.008   0.001   TYR R 209 
 ARG   0.002   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15685 (  166)
  hydrogen bonds       : angle       5.96689 (  498)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       1.30825 (    2)
  covalent geometry    : bond        0.00447 ( 2274)
  covalent geometry    : angle       0.54954 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.234 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.2204
  time to fit residues: 6.8154
Evaluate side-chains
  22 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0170
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.117389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.102938 restraints weight = 2973.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 1.68
r_work: 0.2944 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    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 = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.0752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2275  Z= 0.140
  Angle     :  0.491   5.628   3116  Z= 0.272
  Chirality :  0.038   0.106    382
  Planarity :  0.003   0.022    372
  Dihedral  :  4.363  21.035    320
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  5.33 %
    Favored  : 92.89 %
  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:  2.01 (0.52), residues: 284
  helix:  2.03 (0.35), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.22 (0.83), residues: 63

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 104 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.002   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06527 (  166)
  hydrogen bonds       : angle       4.48519 (  498)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       0.98196 (    2)
  covalent geometry    : bond        0.00290 ( 2274)
  covalent geometry    : angle       0.49009 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.214 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 24
  average time/residue: 0.1908
  time to fit residues: 5.3599
Evaluate side-chains
  22 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0970
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3232 r_free = 0.3232 target = 0.117647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.103307 restraints weight = 2969.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.62
r_work: 0.2953 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.088         |
| 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) = 0.088         |
| 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: 0.8410
moved from start:          0.0915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2275  Z= 0.135
  Angle     :  0.477   5.494   3116  Z= 0.263
  Chirality :  0.038   0.104    382
  Planarity :  0.003   0.021    372
  Dihedral  :  4.331  20.810    320
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  :  7.56 %
    Favored  : 89.33 %
  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:  2.08 (0.51), residues: 284
  helix:  2.08 (0.35), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.22 (0.82), residues: 63

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 104 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06157 (  166)
  hydrogen bonds       : angle       4.28139 (  498)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.98240 (    2)
  covalent geometry    : bond        0.00288 ( 2274)
  covalent geometry    : angle       0.47687 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.244 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 26
  average time/residue: 0.1921
  time to fit residues: 5.8850
Evaluate side-chains
  25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0670
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3233 r_free = 0.3233 target = 0.117738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.103230 restraints weight = 2965.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.66
r_work: 0.2950 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    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 = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2275  Z= 0.132
  Angle     :  0.469   5.487   3116  Z= 0.258
  Chirality :  0.038   0.103    382
  Planarity :  0.003   0.021    372
  Dihedral  :  4.277  20.724    320
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.22 %
    Favored  : 88.00 %
  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:  2.15 (0.52), residues: 284
  helix:  2.16 (0.35), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.31 (0.81), residues: 63

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 104 
 TYR   0.007   0.001   TYR R 308 
 ARG   0.001   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05951 (  166)
  hydrogen bonds       : angle       4.16949 (  498)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.98722 (    2)
  covalent geometry    : bond        0.00282 ( 2274)
  covalent geometry    : angle       0.46832 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.234 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.1906
  time to fit residues: 5.8153
Evaluate side-chains
  25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3205 r_free = 0.3205 target = 0.115842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.101428 restraints weight = 3029.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.62
r_work: 0.2927 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    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 = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2275  Z= 0.145
  Angle     :  0.482   5.491   3116  Z= 0.266
  Chirality :  0.038   0.102    382
  Planarity :  0.003   0.022    372
  Dihedral  :  4.319  20.808    320
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.67 %
    Favored  : 87.56 %
  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:  2.10 (0.52), residues: 284
  helix:  2.12 (0.35), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.34 (0.82), residues: 63

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  61 
 TYR   0.007   0.001   TYR R 209 
 ARG   0.002   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06373 (  166)
  hydrogen bonds       : angle       4.20711 (  498)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       1.07872 (    2)
  covalent geometry    : bond        0.00325 ( 2274)
  covalent geometry    : angle       0.48145 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.252 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 24
  average time/residue: 0.2022
  time to fit residues: 5.6740
Evaluate side-chains
  24 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   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 = 0.3194 r_free = 0.3194 target = 0.114931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.100353 restraints weight = 3018.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.65
r_work: 0.2903 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2275  Z= 0.156
  Angle     :  0.496   5.497   3116  Z= 0.272
  Chirality :  0.039   0.104    382
  Planarity :  0.003   0.022    372
  Dihedral  :  4.348  20.800    320
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.89 %
    Favored  : 85.78 %
  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:  2.04 (0.52), residues: 284
  helix:  2.11 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.44 (0.79), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06634 (  166)
  hydrogen bonds       : angle       4.23515 (  498)
  SS BOND              : bond        0.00129 (    1)
  SS BOND              : angle       1.17958 (    2)
  covalent geometry    : bond        0.00357 ( 2274)
  covalent geometry    : angle       0.49479 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.243 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 24
  average time/residue: 0.1538
  time to fit residues: 4.5226
Evaluate side-chains
  25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0980
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3231 r_free = 0.3231 target = 0.117718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.103022 restraints weight = 3039.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.66
r_work: 0.2945 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    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 = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2275  Z= 0.130
  Angle     :  0.470   5.455   3116  Z= 0.258
  Chirality :  0.038   0.105    382
  Planarity :  0.003   0.022    372
  Dihedral  :  4.212  20.827    320
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.33 %
    Favored  : 84.89 %
  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:  2.22 (0.51), residues: 284
  helix:  2.22 (0.35), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.34 (0.79), residues: 63

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 104 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05858 (  166)
  hydrogen bonds       : angle       4.11161 (  498)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       1.01102 (    2)
  covalent geometry    : bond        0.00276 ( 2274)
  covalent geometry    : angle       0.46958 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.240 
Fit side-chains
REVERT: R  231 GLN cc_start: 0.7947 (tt0) cc_final: 0.7709 (tm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 25
  average time/residue: 0.1845
  time to fit residues: 5.4796
Evaluate side-chains
  25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.114032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.099371 restraints weight = 3085.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.65
r_work: 0.2896 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2275  Z= 0.166
  Angle     :  0.502   5.496   3116  Z= 0.276
  Chirality :  0.039   0.110    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.362  20.762    320
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.22 %
    Favored  : 84.00 %
  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:  2.04 (0.51), residues: 284
  helix:  2.15 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -1.51 (0.75), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 209 
 ARG   0.002   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06806 (  166)
  hydrogen bonds       : angle       4.24821 (  498)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       1.18045 (    2)
  covalent geometry    : bond        0.00389 ( 2274)
  covalent geometry    : angle       0.50140 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.240 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1356
  time to fit residues: 3.9239
Evaluate side-chains
  23 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    0.0170
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.3418

-------------------------------------------------------------------------------
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 = 0.3264 r_free = 0.3264 target = 0.120259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.105465 restraints weight = 3019.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.68
r_work: 0.2980 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2275  Z= 0.115
  Angle     :  0.447   5.445   3116  Z= 0.245
  Chirality :  0.037   0.104    382
  Planarity :  0.003   0.023    372
  Dihedral  :  4.090  20.805    320
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.22 %
    Favored  : 84.44 %
  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:  2.38 (0.51), residues: 284
  helix:  2.36 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.34 (0.76), residues: 64

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 104 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05215 (  166)
  hydrogen bonds       : angle       4.01914 (  498)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       0.97664 (    2)
  covalent geometry    : bond        0.00229 ( 2274)
  covalent geometry    : angle       0.44679 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.241 
Fit side-chains
REVERT: R  227 LYS cc_start: 0.8047 (tttt) cc_final: 0.7678 (ttmm)
REVERT: R  231 GLN cc_start: 0.7953 (tt0) cc_final: 0.7727 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1948
  time to fit residues: 6.7988
Evaluate side-chains
  27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   chunk 24 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.117164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.102551 restraints weight = 2968.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.62
r_work: 0.2942 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    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 = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2275  Z= 0.134
  Angle     :  0.464   5.445   3116  Z= 0.255
  Chirality :  0.038   0.104    382
  Planarity :  0.003   0.022    372
  Dihedral  :  4.166  20.569    320
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 15.56 %
    Favored  : 83.56 %
  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:  2.31 (0.51), residues: 284
  helix:  2.30 (0.35), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.37 (0.77), residues: 63

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   0.007   0.001   PHE R  61 
 TYR   0.007   0.001   TYR R 209 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05858 (  166)
  hydrogen bonds       : angle       4.07386 (  498)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       1.03419 (    2)
  covalent geometry    : bond        0.00294 ( 2274)
  covalent geometry    : angle       0.46378 ( 3114)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.239 
Fit side-chains
REVERT: R  227 LYS cc_start: 0.8039 (tttt) cc_final: 0.7676 (ttmm)
REVERT: R  231 GLN cc_start: 0.8014 (tt0) cc_final: 0.7781 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 26
  average time/residue: 0.2265
  time to fit residues: 6.7585
Evaluate side-chains
  26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.114831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.100406 restraints weight = 2998.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.60
r_work: 0.2913 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    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 = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2275  Z= 0.148
  Angle     :  0.481   5.457   3116  Z= 0.264
  Chirality :  0.038   0.106    382
  Planarity :  0.003   0.022    372
  Dihedral  :  4.267  20.641    320
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.67 %
    Favored  : 83.56 %
  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:  2.16 (0.52), residues: 284
  helix:  2.08 (0.35), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.24 (0.82), residues: 58

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  61 
 TYR   0.007   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06466 (  166)
  hydrogen bonds       : angle       4.17001 (  498)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       1.11109 (    2)
  covalent geometry    : bond        0.00337 ( 2274)
  covalent geometry    : angle       0.47989 ( 3114)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1581.35 seconds
wall clock time: 28 minutes 10.11 seconds (1690.11 seconds total)