Starting phenix.real_space_refine
on Thu Oct 22 21:25:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lv7_63415/10_2026/9lv7_63415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lv7_63415/10_2026/9lv7_63415.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lv7_63415/10_2026/9lv7_63415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lv7_63415/10_2026/9lv7_63415.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lv7_63415/10_2026/9lv7_63415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lv7_63415/10_2026/9lv7_63415.map"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     P     110      5.49       5
     S      13      5.16       5
     C    3278      2.51       5
     N    1035      2.21       5
     O    1390      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5826
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 2351
          Classifications: {'RNA': 110}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 47, 'rna3p_pyr': 44}
          Link IDs: {'rna2p': 19, 'rna3p': 90}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 3475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3475
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 13, 'TRANS': 411}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 1.45, per 1000 atoms: 0.25
  Number of scatterers: 5826
  At special positions: 0
  Unit cell: (71.25, 96.75, 135.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     P     110     15.00
     O    1390      8.00
     N    1035      7.00
     C    3278      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.36
  Conformation dependent library (CDL) restraints added in 194.6 milliseconds
  

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  814

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 4 sheets defined
      53.6% alpha, 10.8% beta
      36 base pairs and 60 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 31
    Processing helix  chain 'A' and resid 32 through 39
    Processing helix  chain 'A' and resid 76 through 102
      removed outlier: 3.938A  pdb=" N   GLY A  92 " --> pdb=" O   GLU A  88 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   HIS A  93 " --> pdb=" O   TYR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 132
    Processing helix  chain 'A' and resid 144 through 148
      removed outlier: 4.194A  pdb=" N   LEU A 148 " --> pdb=" O   PHE A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 162
    Processing helix  chain 'A' and resid 167 through 179
    Processing helix  chain 'A' and resid 185 through 193
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 237 through 246
      removed outlier: 3.733A  pdb=" N   MET A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 259
    Processing helix  chain 'A' and resid 276 through 280
    Processing helix  chain 'A' and resid 282 through 291
    Processing helix  chain 'A' and resid 336 through 368
      removed outlier: 3.853A  pdb=" N   LEU A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 364 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 385
    Processing helix  chain 'A' and resid 391 through 404
    Processing helix  chain 'A' and resid 405 through 413
      removed outlier: 4.186A  pdb=" N   LYS A 409 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 425
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 74
      removed outlier: 3.858A  pdb=" N   LYS A  53 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   TYR A  74 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A  45 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264
      removed outlier: 3.945A  pdb=" N   ILE A 309 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 316 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS A 311 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142
      removed outlier: 4.808A  pdb=" N   GLU A 297 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322
      removed outlier: 3.595A  pdb=" N   ILE A 327 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)

    178 hydrogen bonds defined for protein.
    501 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      87 hydrogen bonds
      146 hydrogen bond angles
      0 basepair planarities
      36 basepair parallelities
      60 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 898
        1.33 -     1.45: 2204
        1.45 -     1.57: 2835
        1.57 -     1.69: 216
        1.69 -     1.82: 22
  Bond restraints: 6175
  Sorted by residual:
  bond pdb=" CA  ALA A 270 "
       pdb=" C   ALA A 270 "
    ideal  model  delta    sigma   weight residual
    1.524  1.434  0.090 1.31e-02 5.83e+03 4.72e+01
  bond pdb=" C1'   U R 224 "
       pdb=" N1    U R 224 "
    ideal  model  delta    sigma   weight residual
    1.483  1.558 -0.075 1.50e-02 4.44e+03 2.51e+01
  bond pdb=" CA  PHE A 273 "
       pdb=" C   PHE A 273 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 1.23e-02 6.61e+03 1.24e+01
  bond pdb=" CA  LEU A 272 "
       pdb=" CB  LEU A 272 "
    ideal  model  delta    sigma   weight residual
    1.530  1.471  0.059 1.69e-02 3.50e+03 1.22e+01
  bond pdb=" CA  ARG A 266 "
       pdb=" C   ARG A 266 "
    ideal  model  delta    sigma   weight residual
    1.523  1.478  0.045 1.31e-02 5.83e+03 1.18e+01
  ... (remaining 6170 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 8403
        1.85 -     3.70: 413
        3.70 -     5.55: 25
        5.55 -     7.40: 6
        7.40 -     9.25: 4
  Bond angle restraints: 8851
  Sorted by residual:
  angle pdb=" C   PHE A 273 "
        pdb=" N   ILE A 274 "
        pdb=" CA  ILE A 274 "
      ideal   model   delta    sigma   weight residual
     122.59  129.39   -6.80 1.10e+00 8.26e-01 3.82e+01
  angle pdb=" CA  PHE A 273 "
        pdb=" C   PHE A 273 "
        pdb=" N   ILE A 274 "
      ideal   model   delta    sigma   weight residual
     116.37  122.55   -6.18 1.19e+00 7.06e-01 2.70e+01
  angle pdb=" C   ASP A 312 "
        pdb=" CA  ASP A 312 "
        pdb=" CB  ASP A 312 "
      ideal   model   delta    sigma   weight residual
     117.23  110.58    6.65 1.36e+00 5.41e-01 2.39e+01
  angle pdb=" O4'   G R 227 "
        pdb=" C4'   G R 227 "
        pdb=" C3'   G R 227 "
      ideal   model   delta    sigma   weight residual
     106.10  102.40    3.70 8.00e-01 1.56e+00 2.13e+01
  angle pdb=" O2    C R 267 "
        pdb=" C2    C R 267 "
        pdb=" N3    C R 267 "
      ideal   model   delta    sigma   weight residual
     121.90  118.95    2.95 7.00e-01 2.04e+00 1.78e+01
  ... (remaining 8846 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.31: 3506
       35.31 -    70.63: 346
       70.63 -   105.94: 29
      105.94 -   141.25: 3
      141.25 -   176.57: 1
  Dihedral angle restraints: 3885
    sinusoidal: 2622
      harmonic: 1263
  Sorted by residual:
  dihedral pdb=" O4'   C R 229 "
           pdb=" C1'   C R 229 "
           pdb=" N1    C R 229 "
           pdb=" C2    C R 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -87.24  -72.76     1      1.50e+01 4.44e-03 3.00e+01
  dihedral pdb=" O4'   C R 228 "
           pdb=" C1'   C R 228 "
           pdb=" N1    C R 228 "
           pdb=" C2    C R 228 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -53.05  -74.95     1      1.70e+01 3.46e-03 2.46e+01
  dihedral pdb=" O4'   U R 243 "
           pdb=" C1'   U R 243 "
           pdb=" N1    U R 243 "
           pdb=" C2    U R 243 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -54.44  -73.56     1      1.70e+01 3.46e-03 2.38e+01
  ... (remaining 3882 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 899
       0.078 -    0.156: 152
       0.156 -    0.235: 8
       0.235 -    0.313: 0
       0.313 -    0.391: 1
  Chirality restraints: 1060
  Sorted by residual:
  chirality pdb=" C3'   A R 225 "
            pdb=" C4'   A R 225 "
            pdb=" O3'   A R 225 "
            pdb=" C2'   A R 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.35   -0.39 2.00e-01 2.50e+01 3.82e+00
  chirality pdb=" CA  ARG A 266 "
            pdb=" N   ARG A 266 "
            pdb=" C   ARG A 266 "
            pdb=" CB  ARG A 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C3'   U R 224 "
            pdb=" C4'   U R 224 "
            pdb=" O3'   U R 224 "
            pdb=" C2'   U R 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1057 not shown)

  Planarity restraints: 714
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 265 "    0.016 2.00e-02 2.50e+03   3.06e-02 9.34e+00
        pdb=" C   TYR A 265 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   TYR A 265 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 266 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  42 "   -0.037 5.00e-02 4.00e+02   5.70e-02 5.20e+00
        pdb=" N   PRO A  43 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  19 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO A  20 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A  20 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  20 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 711 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 598
        2.74 -     3.28: 5317
        3.28 -     3.82: 10230
        3.82 -     4.36: 11601
        4.36 -     4.90: 17671
  Nonbonded interactions: 45417
  Sorted by model distance:
  nonbonded pdb=" O2'   U R 204 "
            pdb=" OP1   G R 206 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG1 THR A 208 "
            pdb=" OD1 ASP A 211 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O2'   A R 210 "
            pdb=" OP1   A R 211 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   PRO A 199 "
            pdb=" NH1 ARG A 203 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" N   GLU A 105 "
            pdb=" OE1 GLU A 105 "
     model   vdw
     2.315 3.120
  ... (remaining 45412 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.080
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6471
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   0.090   6175  Z= 0.283
  Angle     :  0.779   9.246   8851  Z= 0.590
  Chirality :  0.057   0.391   1060
  Planarity :  0.004   0.057    714
  Dihedral  : 22.567 176.569   3071
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  2.84 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 26.15 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.39), residues: 423
  helix:  1.48 (0.36), residues: 212
  sheet: -0.16 (0.69), residues: 53
  loop : -0.70 (0.43), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 306 
 TYR   0.020   0.002   TYR A 323 
 PHE   0.020   0.003   PHE A 308 
 TRP   0.004   0.001   TRP A   8 
 HIS   0.007   0.001   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.28 ( 6175)
  covalent geometry    : angle       0.77876 /  0.59 ( 8851)
  hydrogen bonds       : bond        0.12524 / 13.27 (  265)
  hydrogen bonds       : angle       4.99852 /  6.04 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  229 LYS cc_start: 0.7516 (ttmm) cc_final: 0.7270 (ttpp)
REVERT: A  266 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6942 (ttp80)
REVERT: A  347 MET cc_start: 0.7255 (ttp) cc_final: 0.6859 (ttp)
  outliers start: 4
  outliers final: 1
  residues processed: 69
  average time/residue: 0.1333
  time to fit residues: 10.9355
Evaluate side-chains
  68 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  266 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 50, 19, 30]
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0870
   chunk 2 optimal weight:  100.0000
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0060
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0270
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.2832

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.195532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159931 restraints weight = 9575.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.163729 restraints weight = 5421.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.166276 restraints weight = 3733.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.167960 restraints weight = 2915.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.168893 restraints weight = 2469.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6373
moved from start:          0.0778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6175  Z= 0.115
  Angle     :  0.523   7.913   8851  Z= 0.296
  Chirality :  0.039   0.398   1060
  Planarity :  0.004   0.044    714
  Dihedral  : 22.667 178.498   2194
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 22.10 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.40), residues: 423
  helix:  1.50 (0.36), residues: 214
  sheet:  0.63 (0.67), residues: 53
  loop : -0.49 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 306 
 TYR   0.015   0.001   TYR A  86 
 PHE   0.010   0.002   PHE A  47 
 TRP   0.005   0.001   TRP A 157 
 HIS   0.005   0.001   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00213 /  0.12 ( 6175)
  covalent geometry    : angle       0.52257 /  0.30 ( 8851)
  hydrogen bonds       : bond        0.05813 /  6.36 (  265)
  hydrogen bonds       : angle       3.78129 /  4.46 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  185 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7440 (tttp)
REVERT: A  253 MET cc_start: 0.6515 (tpp) cc_final: 0.6208 (tpt)
REVERT: A  283 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6579 (tt)
REVERT: A  310 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.6065 (t80)
  outliers start: 13
  outliers final: 7
  residues processed: 72
  average time/residue: 0.1195
  time to fit residues: 10.3251
Evaluate side-chains
  75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [49, 43, 6, 8, 38, 21, 36, 10, 1, 2, 50]
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 2 optimal weight:   70.0000
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.3986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.190517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.154197 restraints weight = 9568.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.157709 restraints weight = 5689.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.160283 restraints weight = 4019.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.161627 restraints weight = 3187.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.162832 restraints weight = 2760.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6513
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6175  Z= 0.236
  Angle     :  0.613   8.390   8851  Z= 0.342
  Chirality :  0.042   0.429   1060
  Planarity :  0.005   0.053    714
  Dihedral  : 22.612 179.329   2188
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 22.10 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.39), residues: 423
  helix:  0.93 (0.35), residues: 214
  sheet:  0.65 (0.70), residues: 51
  loop : -0.72 (0.46), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 306 
 TYR   0.020   0.003   TYR A  86 
 PHE   0.027   0.004   PHE A 212 
 TRP   0.012   0.003   TRP A   8 
 HIS   0.015   0.002   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00528 /  0.24 ( 6175)
  covalent geometry    : angle       0.61250 /  0.34 ( 8851)
  hydrogen bonds       : bond        0.07609 /  8.57 (  265)
  hydrogen bonds       : angle       4.11215 /  4.75 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   16 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7851 (m-70)
REVERT: A  185 LYS cc_start: 0.7713 (tmtt) cc_final: 0.7504 (tttm)
REVERT: A  253 MET cc_start: 0.6572 (tpp) cc_final: 0.6264 (tpt)
REVERT: A  347 MET cc_start: 0.7211 (ttp) cc_final: 0.6883 (ttp)
  outliers start: 20
  outliers final: 14
  residues processed: 76
  average time/residue: 0.1162
  time to fit residues: 10.7429
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   16 HIS
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [27, 46, 39, 33, 2, 11, 1, 38, 44, 8, 17]
   chunk 27 optimal weight:    0.3980
   chunk 46 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:  100.0000
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 8 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.193291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.157188 restraints weight = 9582.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.160940 restraints weight = 5600.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.163152 restraints weight = 3913.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.165091 restraints weight = 3123.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.165849 restraints weight = 2647.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6447
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6175  Z= 0.133
  Angle     :  0.504   8.023   8851  Z= 0.288
  Chirality :  0.038   0.400   1060
  Planarity :  0.005   0.043    714
  Dihedral  : 22.579 179.142   2188
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 22.91 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.40), residues: 423
  helix:  1.24 (0.36), residues: 214
  sheet:  0.73 (0.66), residues: 53
  loop : -0.64 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 111 
 TYR   0.018   0.002   TYR A 279 
 PHE   0.023   0.002   PHE A 376 
 TRP   0.010   0.002   TRP A   8 
 HIS   0.005   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 ( 6175)
  covalent geometry    : angle       0.50374 /  0.29 ( 8851)
  hydrogen bonds       : bond        0.06046 /  6.77 (  265)
  hydrogen bonds       : angle       3.80775 /  4.48 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  185 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7455 (tttp)
REVERT: A  253 MET cc_start: 0.6529 (tpp) cc_final: 0.6210 (tpt)
REVERT: A  310 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.6114 (t80)
REVERT: A  347 MET cc_start: 0.7120 (ttp) cc_final: 0.6742 (ttp)
REVERT: A  355 LYS cc_start: 0.7438 (mttm) cc_final: 0.7180 (mtmm)
  outliers start: 20
  outliers final: 13
  residues processed: 76
  average time/residue: 0.1219
  time to fit residues: 11.0946
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  377 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [51, 17, 5, 11, 38, 1, 9, 19, 31, 15, 50]
   chunk 51 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.192361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.156066 restraints weight = 9638.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.159796 restraints weight = 5619.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.162379 restraints weight = 3920.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.163853 restraints weight = 3071.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.165132 restraints weight = 2641.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6175  Z= 0.161
  Angle     :  0.515   8.084   8851  Z= 0.293
  Chirality :  0.038   0.407   1060
  Planarity :  0.005   0.044    714
  Dihedral  : 22.536 179.467   2188
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 23.45 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.40), residues: 423
  helix:  1.20 (0.36), residues: 214
  sheet:  0.63 (0.66), residues: 53
  loop : -0.63 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 410 
 TYR   0.015   0.002   TYR A 279 
 PHE   0.027   0.003   PHE A 376 
 TRP   0.011   0.002   TRP A   8 
 HIS   0.007   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 ( 6175)
  covalent geometry    : angle       0.51523 /  0.29 ( 8851)
  hydrogen bonds       : bond        0.06322 /  7.13 (  265)
  hydrogen bonds       : angle       3.81116 /  4.45 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  158 CYS cc_start: 0.6941 (p) cc_final: 0.6722 (p)
REVERT: A  185 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7441 (tttm)
REVERT: A  253 MET cc_start: 0.6560 (tpp) cc_final: 0.6240 (tpt)
REVERT: A  310 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.6118 (t80)
REVERT: A  347 MET cc_start: 0.7164 (ttp) cc_final: 0.6800 (ttp)
  outliers start: 21
  outliers final: 17
  residues processed: 78
  average time/residue: 0.1253
  time to fit residues: 11.7600
Evaluate side-chains
  82 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  377 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [22, 26, 36, 50, 10, 3, 28, 1, 42, 39, 20]
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 50 optimal weight:    0.6980
   chunk 10 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0170
   overall best weight:    0.5016

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.194116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.158284 restraints weight = 9635.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.161918 restraints weight = 5639.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.164561 restraints weight = 3921.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.166049 restraints weight = 3087.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.167282 restraints weight = 2641.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6175  Z= 0.116
  Angle     :  0.469   7.769   8851  Z= 0.269
  Chirality :  0.036   0.389   1060
  Planarity :  0.004   0.039    714
  Dihedral  : 22.501 178.505   2188
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 23.45 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.41), residues: 423
  helix:  1.41 (0.36), residues: 214
  sheet:  0.72 (0.67), residues: 53
  loop : -0.55 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 260 
 TYR   0.017   0.002   TYR A 279 
 PHE   0.014   0.002   PHE A 376 
 TRP   0.009   0.002   TRP A 157 
 HIS   0.004   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.12 ( 6175)
  covalent geometry    : angle       0.46936 /  0.27 ( 8851)
  hydrogen bonds       : bond        0.05568 /  6.25 (  265)
  hydrogen bonds       : angle       3.63730 /  4.30 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  100 GLU cc_start: 0.7660 (tp30) cc_final: 0.7458 (tp30)
REVERT: A  158 CYS cc_start: 0.6877 (p) cc_final: 0.6669 (p)
REVERT: A  185 LYS cc_start: 0.7629 (tmtt) cc_final: 0.7426 (tttm)
REVERT: A  253 MET cc_start: 0.6567 (tpp) cc_final: 0.6195 (tpt)
REVERT: A  310 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.6047 (t80)
REVERT: A  379 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6635 (ttmm)
  outliers start: 21
  outliers final: 15
  residues processed: 80
  average time/residue: 0.1190
  time to fit residues: 11.3158
Evaluate side-chains
  80 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   16 HIS
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  377 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [6, 35, 13, 37, 40, 0, 41, 1, 34, 8, 31]
   chunk 6 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.192192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.155701 restraints weight = 9415.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.159505 restraints weight = 5335.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.162051 restraints weight = 3658.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.163405 restraints weight = 2855.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.164595 restraints weight = 2466.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6175  Z= 0.139
  Angle     :  0.499   7.884   8851  Z= 0.284
  Chirality :  0.037   0.403   1060
  Planarity :  0.004   0.040    714
  Dihedral  : 22.474 178.871   2188
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 24.26 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.40), residues: 423
  helix:  1.28 (0.36), residues: 214
  sheet:  0.73 (0.67), residues: 53
  loop : -0.68 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 260 
 TYR   0.024   0.002   TYR A 279 
 PHE   0.021   0.002   PHE A 376 
 TRP   0.009   0.002   TRP A   8 
 HIS   0.006   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 6175)
  covalent geometry    : angle       0.49888 /  0.28 ( 8851)
  hydrogen bonds       : bond        0.05947 /  6.74 (  265)
  hydrogen bonds       : angle       3.67701 /  4.30 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  158 CYS cc_start: 0.6885 (p) cc_final: 0.6657 (p)
REVERT: A  185 LYS cc_start: 0.7649 (tmtt) cc_final: 0.7440 (tttm)
REVERT: A  200 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7688 (mmmt)
REVERT: A  253 MET cc_start: 0.6585 (tpp) cc_final: 0.6235 (tpt)
REVERT: A  300 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7883 (p)
REVERT: A  310 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.6059 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 78
  average time/residue: 0.1101
  time to fit residues: 10.4536
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  377 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [22, 24, 52, 25, 51, 10, 31, 15, 41, 20, 48]
   chunk 22 optimal weight:    0.1980
   chunk 24 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0050
   chunk 10 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0040
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.2206

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.195558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.159925 restraints weight = 9671.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.163616 restraints weight = 5614.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.166083 restraints weight = 3901.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.167420 restraints weight = 3087.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.168588 restraints weight = 2664.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6175  Z= 0.095
  Angle     :  0.454   7.519   8851  Z= 0.260
  Chirality :  0.035   0.380   1060
  Planarity :  0.004   0.039    714
  Dihedral  : 22.431 177.889   2188
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 24.80 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.41), residues: 423
  helix:  1.48 (0.36), residues: 215
  sheet:  1.04 (0.69), residues: 53
  loop : -0.48 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 410 
 TYR   0.021   0.001   TYR A 384 
 PHE   0.014   0.002   PHE A 328 
 TRP   0.012   0.002   TRP A 157 
 HIS   0.003   0.001   HIS A 386 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00183 /  0.10 ( 6175)
  covalent geometry    : angle       0.45400 /  0.26 ( 8851)
  hydrogen bonds       : bond        0.05063 /  5.68 (  265)
  hydrogen bonds       : angle       3.51648 /  4.21 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  158 CYS cc_start: 0.6740 (p) cc_final: 0.6533 (p)
REVERT: A  185 LYS cc_start: 0.7631 (tmtt) cc_final: 0.7430 (tttm)
REVERT: A  200 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7670 (mmmt)
REVERT: A  253 MET cc_start: 0.6606 (tpp) cc_final: 0.6178 (tpt)
REVERT: A  310 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6026 (t80)
REVERT: A  379 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6624 (ttmm)
  outliers start: 15
  outliers final: 11
  residues processed: 76
  average time/residue: 0.1209
  time to fit residues: 11.1464
Evaluate side-chains
  78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   16 HIS
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  390 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [22, 50, 34, 12, 30, 15, 9, 52, 18, 39, 3]
   chunk 22 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 3 optimal weight:   10.0000
   overall best weight:    0.4938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.194897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.158627 restraints weight = 9842.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.162427 restraints weight = 5716.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.164721 restraints weight = 3980.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.166324 restraints weight = 3151.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.167538 restraints weight = 2693.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6405
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6175  Z= 0.116
  Angle     :  0.468   7.634   8851  Z= 0.265
  Chirality :  0.035   0.394   1060
  Planarity :  0.004   0.042    714
  Dihedral  : 22.390 178.254   2188
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 24.80 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.41), residues: 423
  helix:  1.49 (0.36), residues: 215
  sheet:  1.13 (0.68), residues: 53
  loop : -0.52 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 260 
 TYR   0.017   0.002   TYR A 384 
 PHE   0.015   0.002   PHE A 376 
 TRP   0.008   0.002   TRP A   8 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.12 ( 6175)
  covalent geometry    : angle       0.46758 /  0.27 ( 8851)
  hydrogen bonds       : bond        0.05292 /  6.03 (  265)
  hydrogen bonds       : angle       3.51524 /  4.16 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  158 CYS cc_start: 0.6711 (p) cc_final: 0.6490 (p)
REVERT: A  200 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7684 (mmmt)
REVERT: A  253 MET cc_start: 0.6668 (tpp) cc_final: 0.6354 (tpp)
REVERT: A  300 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7827 (p)
REVERT: A  310 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.6039 (t80)
REVERT: A  355 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7395 (mtmm)
REVERT: A  379 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6626 (ttmm)
  outliers start: 17
  outliers final: 13
  residues processed: 79
  average time/residue: 0.1202
  time to fit residues: 11.4980
Evaluate side-chains
  75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   16 HIS
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  377 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [32, 48, 11, 6, 22, 18, 5, 16, 43, 27, 36]
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 16 optimal weight:    0.4980
   chunk 43 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.193858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.157349 restraints weight = 9848.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.161060 restraints weight = 5780.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.163421 restraints weight = 4045.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.164779 restraints weight = 3190.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.165960 restraints weight = 2769.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6439
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6175  Z= 0.140
  Angle     :  0.491   7.831   8851  Z= 0.279
  Chirality :  0.037   0.406   1060
  Planarity :  0.004   0.040    714
  Dihedral  : 22.401 178.604   2188
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 24.80 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.41), residues: 423
  helix:  1.35 (0.36), residues: 215
  sheet:  1.13 (0.67), residues: 53
  loop : -0.69 (0.48), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 260 
 TYR   0.016   0.002   TYR A 180 
 PHE   0.020   0.002   PHE A 376 
 TRP   0.008   0.002   TRP A   8 
 HIS   0.004   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 ( 6175)
  covalent geometry    : angle       0.49113 /  0.28 ( 8851)
  hydrogen bonds       : bond        0.05736 /  6.54 (  265)
  hydrogen bonds       : angle       3.59759 /  4.24 (  647)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  253 MET cc_start: 0.6697 (tpp) cc_final: 0.6371 (tpp)
REVERT: A  300 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7853 (p)
REVERT: A  310 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6041 (t80)
REVERT: A  379 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6613 (tptm)
  outliers start: 17
  outliers final: 11
  residues processed: 71
  average time/residue: 0.1097
  time to fit residues: 9.5504
Evaluate side-chains
  71 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  423 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks: [33, 20, 26, 43, 46, 23, 47, 40, 11, 49, 52]
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 26 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6158

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.194384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.158175 restraints weight = 9573.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.161854 restraints weight = 5641.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.164249 restraints weight = 3955.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.165771 restraints weight = 3131.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.166703 restraints weight = 2696.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6175  Z= 0.125
  Angle     :  0.483   7.799   8851  Z= 0.274
  Chirality :  0.036   0.400   1060
  Planarity :  0.004   0.039    714
  Dihedral  : 22.399 178.615   2188
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 24.80 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.41), residues: 423
  helix:  1.32 (0.36), residues: 215
  sheet:  1.14 (0.67), residues: 53
  loop : -0.69 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 260 
 TYR   0.017   0.002   TYR A 323 
 PHE   0.017   0.002   PHE A 376 
 TRP   0.008   0.002   TRP A   8 
 HIS   0.004   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.13 ( 6175)
  covalent geometry    : angle       0.48252 /  0.27 ( 8851)
  hydrogen bonds       : bond        0.05587 /  6.35 (  265)
  hydrogen bonds       : angle       3.55259 /  4.19 (  647)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1123.90 seconds
wall clock time: 20 minutes 2.00 seconds (1202.00 seconds total)