Starting phenix.real_space_refine
on Fri Aug 22 12:40:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7abk_11698/08_2025/7abk_11698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7abk_11698/08_2025/7abk_11698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7abk_11698/08_2025/7abk_11698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7abk_11698/08_2025/7abk_11698.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7abk_11698/08_2025/7abk_11698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7abk_11698/08_2025/7abk_11698.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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       2      5.16       5
     C     977      2.51       5
     N     289      2.21       5
     O     306      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1574
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1574
          Classifications: {'peptide': 196}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 0.75, per 1000 atoms: 0.48
  Number of scatterers: 1574
  At special positions: 0
  Unit cell: (69.6287, 180.364, 52.0118, 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       2     16.00
     O     306      8.00
     N     289      7.00
     C     977      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: 0.17
  Conformation dependent library (CDL) restraints added in 66.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  378

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 0 sheets defined
      89.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 80
      removed outlier: 3.593A  pdb=" N   LEU A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A  29 " --> pdb=" O   PRO A  25 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU A  30 " --> pdb=" O   GLU A  26 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ILE A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 155
      removed outlier: 3.570A  pdb=" N   ALA A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLN A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   SER A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   TYR A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   ALA A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU A 114 " --> pdb=" O   GLU A 110 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLN A 135 " --> pdb=" O   GLU A 131 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ASN A 137 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   LEU A 138 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN A 150 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE A 155 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 186
      removed outlier: 3.500A  pdb=" N   ASN A 186 " --> pdb=" O   ARG A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 216

    141 hydrogen bonds defined for protein.
    423 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: 0.21

  Time building geometry restraints manager: 0.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 558
        1.34 -     1.46: 133
        1.46 -     1.57: 895
        1.57 -     1.69: 0
        1.69 -     1.80: 4
  Bond restraints: 1590
  Sorted by residual:
  bond pdb=" N   LYS A 151 "
       pdb=" CA  LYS A 151 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.77e+00
  bond pdb=" N   ILE A 152 "
       pdb=" CA  ILE A 152 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.29e-02 6.01e+03 7.12e+00
  bond pdb=" N   PHE A  54 "
       pdb=" CA  PHE A  54 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 4.98e+00
  bond pdb=" N   GLU A 153 "
       pdb=" CA  GLU A 153 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.029 1.30e-02 5.92e+03 4.81e+00
  bond pdb=" CA  THR A  53 "
       pdb=" C   THR A  53 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.019 1.35e-02 5.49e+03 2.00e+00
  ... (remaining 1585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 2037
        1.41 -     2.82: 77
        2.82 -     4.23: 16
        4.23 -     5.64: 3
        5.64 -     7.05: 1
  Bond angle restraints: 2134
  Sorted by residual:
  angle pdb=" N   GLU A 153 "
        pdb=" CA  GLU A 153 "
        pdb=" C   GLU A 153 "
      ideal   model   delta    sigma   weight residual
     112.23  105.18    7.05 1.26e+00 6.30e-01 3.13e+01
  angle pdb=" N   PHE A  54 "
        pdb=" CA  PHE A  54 "
        pdb=" C   PHE A  54 "
      ideal   model   delta    sigma   weight residual
     111.07  106.74    4.33 1.07e+00 8.73e-01 1.64e+01
  angle pdb=" N   ALA A  52 "
        pdb=" CA  ALA A  52 "
        pdb=" C   ALA A  52 "
      ideal   model   delta    sigma   weight residual
     111.02  115.79   -4.77 1.22e+00 6.72e-01 1.53e+01
  angle pdb=" N   ILE A 152 "
        pdb=" CA  ILE A 152 "
        pdb=" C   ILE A 152 "
      ideal   model   delta    sigma   weight residual
     112.80  109.11    3.69 1.15e+00 7.56e-01 1.03e+01
  angle pdb=" C   THR A  53 "
        pdb=" CA  THR A  53 "
        pdb=" CB  THR A  53 "
      ideal   model   delta    sigma   weight residual
     110.67  105.27    5.40 1.92e+00 2.71e-01 7.91e+00
  ... (remaining 2129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 891
       17.40 -    34.80: 93
       34.80 -    52.20: 17
       52.20 -    69.60: 8
       69.60 -    87.00: 4
  Dihedral angle restraints: 1013
    sinusoidal: 436
      harmonic: 577
  Sorted by residual:
  dihedral pdb=" CA  ASP A 160 "
           pdb=" C   ASP A 160 "
           pdb=" N   ASN A 161 "
           pdb=" CA  ASN A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.23   15.77     0      5.00e+00 4.00e-02 9.94e+00
  dihedral pdb=" CA  LYS A 151 "
           pdb=" CB  LYS A 151 "
           pdb=" CG  LYS A 151 "
           pdb=" CD  LYS A 151 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.17  -55.83     3      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CA  LEU A 159 "
           pdb=" C   LEU A 159 "
           pdb=" N   ASP A 160 "
           pdb=" CA  ASP A 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.87   15.13     0      5.00e+00 4.00e-02 9.16e+00
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 186
       0.039 -    0.077: 39
       0.077 -    0.116: 9
       0.116 -    0.154: 1
       0.154 -    0.192: 1
  Chirality restraints: 236
  Sorted by residual:
  chirality pdb=" CA  ALA A  52 "
            pdb=" N   ALA A  52 "
            pdb=" C   ALA A  52 "
            pdb=" CB  ALA A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CA  ILE A 152 "
            pdb=" N   ILE A 152 "
            pdb=" C   ILE A 152 "
            pdb=" CB  ILE A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  chirality pdb=" CA  PHE A  54 "
            pdb=" N   PHE A  54 "
            pdb=" C   PHE A  54 "
            pdb=" CB  PHE A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.63   -0.12 2.00e-01 2.50e+01 3.33e-01
  ... (remaining 233 not shown)

  Planarity restraints: 284
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 150 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.13e+00
        pdb=" C   GLN A 150 "    0.031 2.00e-02 2.50e+03
        pdb=" O   GLN A 150 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS A 151 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 188 "    0.016 5.00e-02 4.00e+02   2.41e-02 9.31e-01
        pdb=" N   PRO A 189 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 152 "   -0.004 2.00e-02 2.50e+03   8.67e-03 7.52e-01
        pdb=" C   ILE A 152 "    0.015 2.00e-02 2.50e+03
        pdb=" O   ILE A 152 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   GLU A 153 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 281 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 477
        2.83 -     3.35: 1780
        3.35 -     3.87: 2446
        3.87 -     4.38: 2475
        4.38 -     4.90: 4008
  Nonbonded interactions: 11186
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  26 "
            pdb=" CD1 LEU A 143 "
     model   vdw
     2.315 3.460
  nonbonded pdb=" O   SER A  96 "
            pdb=" OG  SER A  99 "
     model   vdw
     2.436 3.040
  nonbonded pdb=" N   GLU A  30 "
            pdb=" OE1 GLU A  30 "
     model   vdw
     2.443 3.120
  nonbonded pdb=" OD1 ASN A 161 "
            pdb=" OG  SER A 163 "
     model   vdw
     2.453 3.040
  nonbonded pdb=" NH1 ARG A  44 "
            pdb=" OE2 GLU A 126 "
     model   vdw
     2.503 3.120
  ... (remaining 11181 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=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:             5.980
  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:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.370
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
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   0.034   1590  Z= 0.246
  Angle     :  0.660   7.053   2134  Z= 0.437
  Chirality :  0.037   0.192    236
  Planarity :  0.003   0.024    284
  Dihedral  : 16.299  87.004    635
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  6.17 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.56), residues: 194
  helix:  0.77 (0.36), residues: 169
  sheet:  None (None), residues: 0
  loop :  0.20 (1.53), residues: 25

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  45 
 TYR   0.004   0.001   TYR A 129 
 PHE   0.012   0.003   PHE A 168 
 TRP   0.005   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 1590)
  covalent geometry    : angle       0.65979 ( 2134)
  hydrogen bonds       : bond        0.11663 (  141)
  hydrogen bonds       : angle       4.37533 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.065 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8538 (ttm170)
REVERT: A   58 GLU cc_start: 0.9103 (tt0) cc_final: 0.8547 (tm-30)
REVERT: A   62 ASP cc_start: 0.9021 (m-30) cc_final: 0.6966 (m-30)
REVERT: A  121 GLN cc_start: 0.8566 (mt0) cc_final: 0.8170 (tt0)
REVERT: A  127 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8493 (ttm-80)
REVERT: A  128 LYS cc_start: 0.8914 (tptm) cc_final: 0.8441 (ttpt)
REVERT: A  172 GLU cc_start: 0.8958 (tp30) cc_final: 0.8337 (tp30)
REVERT: A  174 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8218 (ttpt)
REVERT: A  177 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8642 (tm-30)
REVERT: A  179 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8454 (tm-30)
REVERT: A  195 LYS cc_start: 0.9568 (ttmt) cc_final: 0.8970 (tptp)
REVERT: A  198 GLN cc_start: 0.9465 (tt0) cc_final: 0.9051 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 80
  average time/residue: 0.1179
  time to fit residues: 10.0382
Evaluate side-chains
  55 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.098757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.079687 restraints weight = 3922.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.081847 restraints weight = 1794.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.083349 restraints weight = 1144.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.084205 restraints weight = 873.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.084777 restraints weight = 750.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1590  Z= 0.165
  Angle     :  0.562   4.976   2134  Z= 0.306
  Chirality :  0.031   0.104    236
  Planarity :  0.004   0.028    284
  Dihedral  :  5.827  55.115    220
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 17.90 %
    Favored  : 77.78 %
  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 aren not related in a simple way.
  whole:  3.42 (0.58), residues: 194
  helix:  2.63 (0.37), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.00 (1.23), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  70 
 TYR   0.010   0.002   TYR A 129 
 PHE   0.008   0.001   PHE A 168 
 TRP   0.005   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 1590)
  covalent geometry    : angle       0.56235 ( 2134)
  hydrogen bonds       : bond        0.07874 (  141)
  hydrogen bonds       : angle       3.50651 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7735 (tpp) cc_final: 0.7376 (tpp)
REVERT: A   58 GLU cc_start: 0.8940 (tt0) cc_final: 0.8599 (tm-30)
REVERT: A   62 ASP cc_start: 0.8822 (m-30) cc_final: 0.6964 (m-30)
REVERT: A  100 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8362 (t-90)
REVERT: A  106 LYS cc_start: 0.8835 (mttt) cc_final: 0.8621 (mtmm)
REVERT: A  123 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8117 (pp30)
REVERT: A  128 LYS cc_start: 0.8947 (tptm) cc_final: 0.8548 (ttpt)
REVERT: A  133 LYS cc_start: 0.9284 (ttmm) cc_final: 0.8976 (ttmm)
REVERT: A  174 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8327 (ttmt)
REVERT: A  177 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8715 (tm-30)
REVERT: A  179 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8421 (tm-30)
REVERT: A  195 LYS cc_start: 0.9564 (ttmt) cc_final: 0.9138 (tptt)
REVERT: A  198 GLN cc_start: 0.9194 (tt0) cc_final: 0.8992 (tm-30)
REVERT: A  212 MET cc_start: 0.7985 (tpt) cc_final: 0.6991 (tpt)
  outliers start: 7
  outliers final: 4
  residues processed: 66
  average time/residue: 0.1195
  time to fit residues: 8.4034
Evaluate side-chains
  59 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.103882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.084384 restraints weight = 3944.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.086791 restraints weight = 1815.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.088412 restraints weight = 1134.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.089289 restraints weight = 846.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.090044 restraints weight = 718.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   1590  Z= 0.149
  Angle     :  0.548   6.712   2134  Z= 0.280
  Chirality :  0.029   0.109    236
  Planarity :  0.004   0.036    284
  Dihedral  :  5.316  49.894    220
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 19.75 %
    Favored  : 77.16 %
  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 aren not related in a simple way.
  whole:  4.61 (0.58), residues: 194
  helix:  3.45 (0.37), residues: 173
  sheet:  None (None), residues: 0
  loop : -1.16 (1.12), residues: 21

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 127 
 TYR   0.007   0.001   TYR A 129 
 PHE   0.007   0.001   PHE A 168 
 TRP   0.005   0.001   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 1590)
  covalent geometry    : angle       0.54842 ( 2134)
  hydrogen bonds       : bond        0.06882 (  141)
  hydrogen bonds       : angle       3.14200 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7506 (tpp) cc_final: 0.7213 (tpp)
REVERT: A  123 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8292 (pp30)
REVERT: A  128 LYS cc_start: 0.8824 (tptm) cc_final: 0.8353 (ttpt)
REVERT: A  133 LYS cc_start: 0.9374 (ttmm) cc_final: 0.9105 (ttmm)
REVERT: A  154 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: A  177 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: A  179 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: A  195 LYS cc_start: 0.9572 (ttmt) cc_final: 0.9063 (tptt)
REVERT: A  198 GLN cc_start: 0.9242 (tt0) cc_final: 0.9000 (tm-30)
REVERT: A  200 GLU cc_start: 0.8962 (pp20) cc_final: 0.8649 (pp20)
  outliers start: 5
  outliers final: 5
  residues processed: 62
  average time/residue: 0.1101
  time to fit residues: 7.3296
Evaluate side-chains
  63 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.104785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.085463 restraints weight = 3937.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.087738 restraints weight = 1808.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.089265 restraints weight = 1126.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.090266 restraints weight = 844.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.090736 restraints weight = 709.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   1590  Z= 0.139
  Angle     :  0.526   5.328   2134  Z= 0.272
  Chirality :  0.030   0.114    236
  Planarity :  0.003   0.025    284
  Dihedral  :  5.208  50.558    220
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.07 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.03 (0.57), residues: 194
  helix:  3.73 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.79 (1.18), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 127 
 TYR   0.006   0.001   TYR A 129 
 PHE   0.005   0.001   PHE A 168 
 TRP   0.004   0.001   TRP A  71 
 HIS   0.001   0.001   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 1590)
  covalent geometry    : angle       0.52552 ( 2134)
  hydrogen bonds       : bond        0.06518 (  141)
  hydrogen bonds       : angle       3.06301 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.065 
Fit side-chains
REVERT: A   27 ASP cc_start: 0.9009 (t70) cc_final: 0.8667 (t0)
REVERT: A   36 MET cc_start: 0.7352 (tpp) cc_final: 0.7081 (tpp)
REVERT: A  123 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: A  128 LYS cc_start: 0.8790 (tptm) cc_final: 0.8232 (ttpt)
REVERT: A  133 LYS cc_start: 0.9413 (ttmm) cc_final: 0.9104 (ttmm)
REVERT: A  154 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: A  177 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8745 (tm-30)
REVERT: A  179 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: A  195 LYS cc_start: 0.9565 (ttmt) cc_final: 0.9056 (tptt)
REVERT: A  198 GLN cc_start: 0.9242 (tt0) cc_final: 0.9024 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 62
  average time/residue: 0.1026
  time to fit residues: 6.8546
Evaluate side-chains
  62 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.105133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.085372 restraints weight = 3929.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.087688 restraints weight = 1798.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.089213 restraints weight = 1118.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.090210 restraints weight = 839.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.090742 restraints weight = 709.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.4762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1590  Z= 0.133
  Angle     :  0.515   5.371   2134  Z= 0.264
  Chirality :  0.030   0.113    236
  Planarity :  0.002   0.022    284
  Dihedral  :  5.188  51.764    220
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 25.93 %
    Favored  : 69.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.14 (0.57), residues: 194
  helix:  3.80 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.70 (1.25), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 127 
 TYR   0.004   0.001   TYR A 129 
 PHE   0.005   0.001   PHE A 168 
 TRP   0.003   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 1590)
  covalent geometry    : angle       0.51545 ( 2134)
  hydrogen bonds       : bond        0.06366 (  141)
  hydrogen bonds       : angle       2.97740 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7395 (tpp) cc_final: 0.7119 (tpp)
REVERT: A   55 LYS cc_start: 0.9499 (mmtp) cc_final: 0.8824 (pttt)
REVERT: A  128 LYS cc_start: 0.8773 (tptm) cc_final: 0.8167 (ttpt)
REVERT: A  133 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9254 (ttmm)
REVERT: A  177 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8749 (tm-30)
REVERT: A  179 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: A  195 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9053 (tptt)
  outliers start: 7
  outliers final: 6
  residues processed: 57
  average time/residue: 0.1059
  time to fit residues: 6.5124
Evaluate side-chains
  59 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.103423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.083871 restraints weight = 3992.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.086134 restraints weight = 1877.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.087479 restraints weight = 1183.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.088502 restraints weight = 904.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.088937 restraints weight = 763.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1590  Z= 0.143
  Angle     :  0.546   5.303   2134  Z= 0.279
  Chirality :  0.032   0.114    236
  Planarity :  0.003   0.021    284
  Dihedral  :  5.278  54.366    220
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 25.93 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.15 (0.56), residues: 194
  helix:  3.82 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.86 (1.23), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 127 
 TYR   0.004   0.001   TYR A 129 
 PHE   0.004   0.001   PHE A 168 
 TRP   0.002   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 1590)
  covalent geometry    : angle       0.54587 ( 2134)
  hydrogen bonds       : bond        0.06543 (  141)
  hydrogen bonds       : angle       3.06848 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.043 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.9504 (mmtp) cc_final: 0.8781 (pttt)
REVERT: A  125 LEU cc_start: 0.9125 (mt) cc_final: 0.8888 (mp)
REVERT: A  128 LYS cc_start: 0.8777 (tptm) cc_final: 0.8172 (ttpt)
REVERT: A  133 LYS cc_start: 0.9476 (ttmm) cc_final: 0.9221 (ttmm)
REVERT: A  177 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8744 (tm-30)
REVERT: A  179 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: A  195 LYS cc_start: 0.9567 (ttmt) cc_final: 0.9060 (tptt)
  outliers start: 8
  outliers final: 7
  residues processed: 58
  average time/residue: 0.1008
  time to fit residues: 6.2759
Evaluate side-chains
  61 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.105307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.085824 restraints weight = 3881.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.088133 restraints weight = 1806.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.089603 restraints weight = 1130.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.090304 restraints weight = 858.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.091050 restraints weight = 746.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.5074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1590  Z= 0.130
  Angle     :  0.538   5.973   2134  Z= 0.265
  Chirality :  0.030   0.113    236
  Planarity :  0.003   0.022    284
  Dihedral  :  5.132  52.022    220
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 27.78 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.27 (0.57), residues: 194
  helix:  3.93 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.09 (1.17), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 127 
 TYR   0.003   0.001   TYR A 129 
 PHE   0.004   0.001   PHE A 168 
 TRP   0.004   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 1590)
  covalent geometry    : angle       0.53761 ( 2134)
  hydrogen bonds       : bond        0.06040 (  141)
  hydrogen bonds       : angle       2.92001 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.9476 (mmtp) cc_final: 0.8766 (pttt)
REVERT: A  128 LYS cc_start: 0.8805 (tptm) cc_final: 0.8244 (ttpt)
REVERT: A  133 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9080 (ttmm)
REVERT: A  177 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8769 (tm-30)
REVERT: A  179 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8331 (tm-30)
REVERT: A  195 LYS cc_start: 0.9547 (ttmt) cc_final: 0.9058 (tptt)
  outliers start: 7
  outliers final: 6
  residues processed: 61
  average time/residue: 0.1031
  time to fit residues: 6.7659
Evaluate side-chains
  59 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.1382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.104491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.085190 restraints weight = 3916.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.087438 restraints weight = 1767.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.088936 restraints weight = 1106.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.089831 restraints weight = 835.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.090453 restraints weight = 711.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   1590  Z= 0.131
  Angle     :  0.563   5.984   2134  Z= 0.275
  Chirality :  0.030   0.116    236
  Planarity :  0.003   0.031    284
  Dihedral  :  5.154  52.684    220
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 29.63 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.22 (0.56), residues: 194
  helix:  3.89 (0.36), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.07 (1.17), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  59 
 TYR   0.004   0.001   TYR A 129 
 PHE   0.003   0.001   PHE A 168 
 TRP   0.003   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 1590)
  covalent geometry    : angle       0.56278 ( 2134)
  hydrogen bonds       : bond        0.06082 (  141)
  hydrogen bonds       : angle       3.01610 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.9057 (tp30) cc_final: 0.8795 (mm-30)
REVERT: A   55 LYS cc_start: 0.9492 (mmtp) cc_final: 0.8770 (pttt)
REVERT: A  128 LYS cc_start: 0.8749 (tptm) cc_final: 0.8188 (ttpt)
REVERT: A  133 LYS cc_start: 0.9493 (ttmm) cc_final: 0.9078 (ttmm)
REVERT: A  177 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8745 (tm-30)
REVERT: A  179 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: A  195 LYS cc_start: 0.9560 (ttmt) cc_final: 0.9050 (tptt)
  outliers start: 8
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1040
  time to fit residues: 6.4206
Evaluate side-chains
  60 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.4984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.103630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.084247 restraints weight = 3963.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.086403 restraints weight = 1797.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.087803 restraints weight = 1137.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.088624 restraints weight = 865.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.089234 restraints weight = 743.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.5110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   1590  Z= 0.140
  Angle     :  0.594   6.075   2134  Z= 0.291
  Chirality :  0.031   0.117    236
  Planarity :  0.003   0.030    284
  Dihedral  :  5.253  54.979    220
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 29.01 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.15 (0.56), residues: 194
  helix:  3.83 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -0.99 (1.20), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 127 
 TYR   0.004   0.001   TYR A 129 
 PHE   0.004   0.001   PHE A 168 
 TRP   0.003   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 1590)
  covalent geometry    : angle       0.59400 ( 2134)
  hydrogen bonds       : bond        0.06403 (  141)
  hydrogen bonds       : angle       3.11005 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.9073 (tp30) cc_final: 0.8805 (mm-30)
REVERT: A   55 LYS cc_start: 0.9493 (mmtp) cc_final: 0.8778 (pttt)
REVERT: A  128 LYS cc_start: 0.8779 (tptm) cc_final: 0.8223 (ttpt)
REVERT: A  133 LYS cc_start: 0.9489 (ttmm) cc_final: 0.9038 (ttmm)
REVERT: A  177 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: A  179 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8353 (tm-30)
REVERT: A  195 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9053 (tptt)
REVERT: A  200 GLU cc_start: 0.9044 (pp20) cc_final: 0.8674 (pp20)
  outliers start: 9
  outliers final: 9
  residues processed: 56
  average time/residue: 0.1014
  time to fit residues: 6.1250
Evaluate side-chains
  59 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  100 HIS
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.105260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.086056 restraints weight = 3868.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.088295 restraints weight = 1760.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.089741 restraints weight = 1100.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.090159 restraints weight = 831.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.091015 restraints weight = 751.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.5248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   1590  Z= 0.133
  Angle     :  0.590   6.432   2134  Z= 0.284
  Chirality :  0.030   0.117    236
  Planarity :  0.003   0.029    284
  Dihedral  :  5.217  53.804    220
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 30.25 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.07 (0.56), residues: 194
  helix:  3.79 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.08 (1.19), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 127 
 TYR   0.003   0.001   TYR A 129 
 PHE   0.004   0.001   PHE A 168 
 TRP   0.003   0.000   TRP A  71 
 HIS   0.000   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 1590)
  covalent geometry    : angle       0.59033 ( 2134)
  hydrogen bonds       : bond        0.06141 (  141)
  hydrogen bonds       : angle       3.05319 (  423)

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

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

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  388 Ramachandran restraints generated.
    194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.9485 (mmtp) cc_final: 0.8772 (pttt)
REVERT: A  128 LYS cc_start: 0.8777 (tptm) cc_final: 0.8214 (ttpt)
REVERT: A  133 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9038 (ttmm)
REVERT: A  177 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8728 (tm-30)
REVERT: A  179 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: A  195 LYS cc_start: 0.9558 (ttmt) cc_final: 0.9051 (tptt)
  outliers start: 8
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1107
  time to fit residues: 6.6592
Evaluate side-chains
  59 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  152 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    2.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.102813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.083161 restraints weight = 3929.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.085311 restraints weight = 1871.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.086707 restraints weight = 1190.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.087480 restraints weight = 908.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.087658 restraints weight = 782.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1590  Z= 0.164
  Angle     :  0.608   5.371   2134  Z= 0.306
  Chirality :  0.033   0.122    236
  Planarity :  0.003   0.037    284
  Dihedral  :  5.434  56.958    220
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 29.63 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.78 (0.56), residues: 194
  helix:  3.58 (0.35), residues: 172
  sheet:  None (None), residues: 0
  loop : -1.03 (1.20), residues: 22

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 127 
 TYR   0.005   0.001   TYR A 129 
 PHE   0.004   0.001   PHE A 168 
 TRP   0.001   0.000   TRP A  71 
 HIS   0.001   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 1590)
  covalent geometry    : angle       0.60849 ( 2134)
  hydrogen bonds       : bond        0.07132 (  141)
  hydrogen bonds       : angle       3.30981 (  423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 693.36 seconds
wall clock time: 12 minutes 29.13 seconds (749.13 seconds total)