Starting phenix.real_space_refine
on Fri May  9 13:47:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggm_40013/05_2025/8ggm_40013.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggm_40013/05_2025/8ggm_40013.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/8ggm_40013/05_2025/8ggm_40013.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggm_40013/05_2025/8ggm_40013.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggm_40013/05_2025/8ggm_40013.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggm_40013/05_2025/8ggm_40013.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=   0.029
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      15      5.16       5
     C    1473      2.51       5
     N     352      2.21       5
     O     371      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: 2211
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2196
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 70
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.70, per 1000 atoms: 1.22
  Number of scatterers: 2211
  At special positions: 0
  Unit cell: (59.0036, 87.6377, 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      15     16.00
     O     371      8.00
     N     352      7.00
     C    1473      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: 0.57
  Conformation dependent library (CDL) restraints added in 264.7 milliseconds
  

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  550

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      87.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.881A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.171A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.417A  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
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.614A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.892A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.528A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 186
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 238
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 4.219A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.589A  pdb=" N   ILE R 291 " --> pdb=" O   LEU R 287 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.607A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.757A  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

    173 hydrogen bonds defined for protein.
    519 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: 0.56

  Time building geometry restraints manager: 0.67 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: 664
        1.35 -     1.46: 607
        1.46 -     1.58: 978
        1.58 -     1.70: 0
        1.70 -     1.81: 21
  Bond restraints: 2270
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.82e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.441 -0.047 2.00e-02 2.50e+03 5.58e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.568 -0.045 2.00e-02 2.50e+03 5.17e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 2.00e-02 2.50e+03 4.03e+00
  bond pdb=" CAE G1I R 501 "
       pdb=" CAG G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.506  1.540 -0.034 2.00e-02 2.50e+03 2.89e+00
  ... (remaining 2265 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 3004
        1.23 -     2.45: 79
        2.45 -     3.68: 15
        3.68 -     4.91: 8
        4.91 -     6.14: 3
  Bond angle restraints: 3109
  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  125.51   -3.81 1.80e+00 3.09e-01 4.48e+00
  angle pdb=" C   LEU R  84 "
        pdb=" N   ALA R  85 "
        pdb=" CA  ALA R  85 "
      ideal   model   delta    sigma   weight residual
     122.42  119.35    3.07 1.55e+00 4.16e-01 3.93e+00
  angle pdb=" C   CYS R 285 "
        pdb=" N   TRP R 286 "
        pdb=" CA  TRP R 286 "
      ideal   model   delta    sigma   weight residual
     122.11  119.06    3.05 1.64e+00 3.72e-01 3.45e+00
  angle pdb=" CG  ARG R  63 "
        pdb=" CD  ARG R  63 "
        pdb=" NE  ARG R  63 "
      ideal   model   delta    sigma   weight residual
     112.00  116.00   -4.00 2.20e+00 2.07e-01 3.31e+00
  angle pdb=" CA  LEU R 144 "
        pdb=" CB  LEU R 144 "
        pdb=" CG  LEU R 144 "
      ideal   model   delta    sigma   weight residual
     116.30  122.44   -6.14 3.50e+00 8.16e-02 3.07e+00
  ... (remaining 3104 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 1177
       16.67 -    33.33: 99
       33.33 -    50.00: 17
       50.00 -    66.67: 2
       66.67 -    83.33: 3
  Dihedral angle restraints: 1298
    sinusoidal: 452
      harmonic: 846
  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 -158.00  -22.00     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  ASN R  51 "
           pdb=" CB  ASN R  51 "
           pdb=" CG  ASN R  51 "
           pdb=" OD1 ASN R  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -161.22   71.22     2      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CA  ALA R  85 "
           pdb=" C   ALA R  85 "
           pdb=" N   VAL R  86 "
           pdb=" CA  VAL R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.07  -15.93     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 1295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 238
       0.029 -    0.058: 87
       0.058 -    0.087: 40
       0.087 -    0.117: 12
       0.117 -    0.146: 1
  Chirality restraints: 378
  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    2.54   -0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  TRP R 286 "
            pdb=" N   TRP R 286 "
            pdb=" C   TRP R 286 "
            pdb=" CB  TRP R 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.12e-01
  chirality pdb=" CA  PRO R 138 "
            pdb=" N   PRO R 138 "
            pdb=" C   PRO R 138 "
            pdb=" CB  PRO R 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.02e-01
  ... (remaining 375 not shown)

  Planarity restraints: 374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO R 168 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 287 "   -0.018 5.00e-02 4.00e+02   2.73e-02 1.19e+00
        pdb=" N   PRO R 288 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO R 288 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO R 288 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.018 5.00e-02 4.00e+02   2.67e-02 1.14e+00
        pdb=" N   PRO R 323 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.015 5.00e-02 4.00e+02
  ... (remaining 371 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 613
        2.82 -     3.34: 2174
        3.34 -     3.86: 3515
        3.86 -     4.38: 3713
        4.38 -     4.90: 6868
  Nonbonded interactions: 16883
  Sorted by model distance:
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAK G1I R 501 "
     model   vdw
     2.444 3.040
  nonbonded pdb=" N   GLU R 306 "
            pdb=" OE1 GLU R 306 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" O   ASN R  69 "
            pdb=" OG1 THR R  73 "
     model   vdw
     2.591 3.040
  ... (remaining 16878 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:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.210
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
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   0.052   2271  Z= 0.179
  Angle     :  0.540   6.137   3111  Z= 0.294
  Chirality :  0.038   0.146    378
  Planarity :  0.004   0.035    374
  Dihedral  : 13.214  83.331    745
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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:  2.21 (0.51), residues: 283
  helix:  2.23 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.06 (0.75), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 290 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.009   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16387 (  173)
  hydrogen bonds       : angle       5.75280 (  519)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       1.14605 (    2)
  covalent geometry    : bond        0.00358 ( 2270)
  covalent geometry    : angle       0.53989 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.240 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2767
  time to fit residues: 6.8525
Evaluate side-chains
  20 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0370
   chunk 14 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.115889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.093996 restraints weight = 2829.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 1.57
r_work: 0.2821 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2271  Z= 0.154
  Angle     :  0.510   6.725   3111  Z= 0.283
  Chirality :  0.040   0.128    378
  Planarity :  0.004   0.029    374
  Dihedral  :  4.492  22.676    319
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.17 %
    Favored  : 91.93 %
  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:  2.14 (0.50), residues: 283
  helix:  2.02 (0.34), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.03 (0.75), residues: 57

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   0.010   0.001   PHE R 290 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06878 (  173)
  hydrogen bonds       : angle       4.52056 (  519)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.99563 (    2)
  covalent geometry    : bond        0.00339 ( 2270)
  covalent geometry    : angle       0.50945 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.251 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 22
  average time/residue: 0.2282
  time to fit residues: 5.8085
Evaluate side-chains
  20 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.115086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.092446 restraints weight = 2842.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 1.66
r_work: 0.2791 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2668 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2271  Z= 0.152
  Angle     :  0.490   5.225   3111  Z= 0.273
  Chirality :  0.040   0.129    378
  Planarity :  0.004   0.028    374
  Dihedral  :  4.505  22.827    319
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  8.97 %
    Favored  : 89.24 %
  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:  2.14 (0.50), residues: 283
  helix:  2.02 (0.34), residues: 226
  sheet:  None (None), residues: 0
  loop : -1.07 (0.73), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 290 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.005   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06872 (  173)
  hydrogen bonds       : angle       4.30112 (  519)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       1.07197 (    2)
  covalent geometry    : bond        0.00340 ( 2270)
  covalent geometry    : angle       0.48964 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.223 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 25
  average time/residue: 0.2049
  time to fit residues: 5.9720
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.115333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.092996 restraints weight = 2824.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 1.62
r_work: 0.2800 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2271  Z= 0.145
  Angle     :  0.496   8.495   3111  Z= 0.269
  Chirality :  0.039   0.128    378
  Planarity :  0.003   0.028    374
  Dihedral  :  4.416  22.829    319
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 12.11 %
    Favored  : 87.00 %
  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:  2.40 (0.50), residues: 283
  helix:  2.11 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.74 (0.81), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 290 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06628 (  173)
  hydrogen bonds       : angle       4.20186 (  519)
  SS BOND              : bond        0.00144 (    1)
  SS BOND              : angle       1.01374 (    2)
  covalent geometry    : bond        0.00316 ( 2270)
  covalent geometry    : angle       0.49557 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.218 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 23
  average time/residue: 0.2097
  time to fit residues: 5.5805
Evaluate side-chains
  23 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.112555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.090584 restraints weight = 2902.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 1.58
r_work: 0.2764 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2640 r_free = 0.2640    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2640
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2271  Z= 0.167
  Angle     :  0.515   8.499   3111  Z= 0.282
  Chirality :  0.040   0.131    378
  Planarity :  0.004   0.028    374
  Dihedral  :  4.507  23.130    319
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.11 %
    Favored  : 86.10 %
  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 (0.50), residues: 283
  helix:  2.04 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.74 (0.79), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 290 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07314 (  173)
  hydrogen bonds       : angle       4.26324 (  519)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       1.03597 (    2)
  covalent geometry    : bond        0.00386 ( 2270)
  covalent geometry    : angle       0.51433 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.260 
Fit side-chains
REVERT: R  218 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8026 (m)
  outliers start: 4
  outliers final: 3
  residues processed: 25
  average time/residue: 0.2043
  time to fit residues: 5.9756
Evaluate side-chains
  26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0670
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0030
   chunk 18 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.3728

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.119388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.097068 restraints weight = 2796.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 1.62
r_work: 0.2860 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2271  Z= 0.119
  Angle     :  0.459   7.513   3111  Z= 0.248
  Chirality :  0.038   0.124    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.216  22.643    319
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.56 %
    Favored  : 85.65 %
  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:  2.60 (0.50), residues: 283
  helix:  2.26 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.72 (0.81), residues: 53

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 217 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05493 (  173)
  hydrogen bonds       : angle       3.99193 (  519)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       0.98276 (    2)
  covalent geometry    : bond        0.00235 ( 2270)
  covalent geometry    : angle       0.45880 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.257 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 26
  average time/residue: 0.1947
  time to fit residues: 5.9049
Evaluate side-chains
  23 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.117169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.094881 restraints weight = 2854.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.65
r_work: 0.2826 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2271  Z= 0.131
  Angle     :  0.471   7.633   3111  Z= 0.256
  Chirality :  0.039   0.124    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.276  22.523    319
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.00 %
    Favored  : 84.75 %
  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:  2.58 (0.50), residues: 283
  helix:  2.24 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.72 (0.80), residues: 53

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 290 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06057 (  173)
  hydrogen bonds       : angle       4.03578 (  519)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       0.91165 (    2)
  covalent geometry    : bond        0.00280 ( 2270)
  covalent geometry    : angle       0.47047 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.237 
Fit side-chains
REVERT: R  228 ARG cc_start: 0.8577 (ttt-90) cc_final: 0.8249 (ttt-90)
  outliers start: 5
  outliers final: 4
  residues processed: 25
  average time/residue: 0.2052
  time to fit residues: 5.9847
Evaluate side-chains
  26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   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 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.114769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.092910 restraints weight = 2932.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 1.59
r_work: 0.2804 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2681 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2271  Z= 0.147
  Angle     :  0.484   7.697   3111  Z= 0.265
  Chirality :  0.039   0.127    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.360  22.768    319
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.90 %
    Favored  : 84.30 %
  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:  2.49 (0.50), residues: 283
  helix:  2.19 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.81 (0.77), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 290 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06605 (  173)
  hydrogen bonds       : angle       4.08973 (  519)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       0.92941 (    2)
  covalent geometry    : bond        0.00330 ( 2270)
  covalent geometry    : angle       0.48394 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.248 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7001 (mtt) cc_final: 0.6801 (mtt)
REVERT: R  228 ARG cc_start: 0.8568 (ttt-90) cc_final: 0.8226 (ttt-90)
  outliers start: 4
  outliers final: 4
  residues processed: 25
  average time/residue: 0.2026
  time to fit residues: 5.9062
Evaluate side-chains
  26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0970
   chunk 14 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0670
   overall best weight:    0.2774

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.121447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.099148 restraints weight = 2779.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.62
r_work: 0.2894 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   2271  Z= 0.112
  Angle     :  0.449   7.155   3111  Z= 0.243
  Chirality :  0.037   0.119    378
  Planarity :  0.003   0.026    374
  Dihedral  :  4.106  22.412    319
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.35 %
    Favored  : 83.86 %
  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:  2.73 (0.50), residues: 283
  helix:  2.41 (0.34), residues: 229
  sheet:  None (None), residues: 0
  loop : -0.95 (0.79), residues: 54

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 290 
 TYR   0.006   0.001   TYR R 219 
 ARG   0.001   0.000   ARG R 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04984 (  173)
  hydrogen bonds       : angle       3.86574 (  519)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       0.94365 (    2)
  covalent geometry    : bond        0.00212 ( 2270)
  covalent geometry    : angle       0.44815 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.201 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7078 (mtt) cc_final: 0.6817 (mtt)
REVERT: R  228 ARG cc_start: 0.8514 (ttt-90) cc_final: 0.8178 (ttt-90)
  outliers start: 4
  outliers final: 4
  residues processed: 26
  average time/residue: 0.2286
  time to fit residues: 6.8043
Evaluate side-chains
  26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN
R 231 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.114365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.091785 restraints weight = 2849.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.66
r_work: 0.2785 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2271  Z= 0.155
  Angle     :  0.496   7.712   3111  Z= 0.272
  Chirality :  0.040   0.128    378
  Planarity :  0.003   0.027    374
  Dihedral  :  4.376  22.656    319
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.25 %
    Favored  : 82.96 %
  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:  2.45 (0.50), residues: 283
  helix:  2.17 (0.34), residues: 230
  sheet:  None (None), residues: 0
  loop : -0.89 (0.76), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 158 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R 290 
 TYR   0.008   0.001   TYR R 199 
 ARG   0.002   0.000   ARG R 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06776 (  173)
  hydrogen bonds       : angle       4.08571 (  519)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       0.92105 (    2)
  covalent geometry    : bond        0.00354 ( 2270)
  covalent geometry    : angle       0.49591 ( 3109)

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

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

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  566 Ramachandran restraints generated.
    283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.225 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7073 (mtt) cc_final: 0.6824 (mtt)
REVERT: R  228 ARG cc_start: 0.8557 (ttt-90) cc_final: 0.8214 (ttt-90)
  outliers start: 4
  outliers final: 4
  residues processed: 23
  average time/residue: 0.2184
  time to fit residues: 5.8244
Evaluate side-chains
  25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0170
   chunk 5 optimal weight:    0.0270
   chunk 27 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.119245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.097361 restraints weight = 2780.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.55
r_work: 0.2875 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2271  Z= 0.116
  Angle     :  0.453   7.097   3111  Z= 0.246
  Chirality :  0.038   0.120    378
  Planarity :  0.003   0.026    374
  Dihedral  :  4.167  22.505    319
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.25 %
    Favored  : 82.96 %
  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:  2.70 (0.50), residues: 283
  helix:  2.33 (0.34), residues: 231
  sheet:  None (None), residues: 0
  loop : -0.78 (0.77), residues: 52

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   0.008   0.001   PHE R 290 
 TYR   0.006   0.001   TYR R 209 
 ARG   0.001   0.000   ARG R 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05385 (  173)
  hydrogen bonds       : angle       3.89531 (  519)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       0.92987 (    2)
  covalent geometry    : bond        0.00229 ( 2270)
  covalent geometry    : angle       0.45265 ( 3109)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1606.06 seconds
wall clock time: 28 minutes 33.78 seconds (1713.78 seconds total)