Starting phenix.real_space_refine
on Fri Aug 22 13:36:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h9n_34574/08_2025/8h9n_34574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h9n_34574/08_2025/8h9n_34574.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h9n_34574/08_2025/8h9n_34574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h9n_34574/08_2025/8h9n_34574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h9n_34574/08_2025/8h9n_34574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h9n_34574/08_2025/8h9n_34574.cif"
  }
  resolution = 3.56
  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=   0.011
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      11      5.16       5
     C    2176      2.51       5
     N     560      2.21       5
     O     634      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 3381
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "K"
      Number of atoms: 1573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1573
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 191}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 549
          Classifications: {'peptide': 67}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 62}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "M"
      Number of atoms: 1259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1259
          Classifications: {'peptide': 156}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
  Time building chain proxies: 1.19, per 1000 atoms: 0.35
  Number of scatterers: 3381
  At special positions: 0
  Unit cell: (81.03, 96.36, 207.32, 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      11     16.00
     O     634      8.00
     N     560      7.00
     C    2176      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: 0.30
  Conformation dependent library (CDL) restraints added in 116.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 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:
      15 helices and 1 sheets defined
      72.7% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'K' and resid 19 through 30
      Proline residue:  K  27  - end of helix
    Processing helix  chain 'K' and resid 32 through 48
    Processing helix  chain 'K' and resid 54 through 121
      removed outlier: 3.900A  pdb=" N   PHE K  58 " --> pdb=" O   SER K  54 " (cutoff:3.500A)
      Proline residue:  K  76  - end of helix
    Processing helix  chain 'K' and resid 122 through 182
    Processing helix  chain 'K' and resid 194 through 206
      removed outlier: 3.789A  pdb=" N   LEU K 201 " --> pdb=" O   CYS K 197 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 41 through 55
    Processing helix  chain 'L' and resid 67 through 83
      removed outlier: 4.318A  pdb=" N   ARG L  73 " --> pdb=" O   GLN L  69 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 12 through 18
      removed outlier: 3.690A  pdb=" N   ILE M  18 " --> pdb=" O   ALA M  14 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 23 through 43
    Processing helix  chain 'M' and resid 53 through 58
    Processing helix  chain 'M' and resid 64 through 75
    Processing helix  chain 'M' and resid 85 through 123
      removed outlier: 3.896A  pdb=" N   VAL M  89 " --> pdb=" O   TYR M  85 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 126 through 130
      removed outlier: 3.690A  pdb=" N   MET M 130 " --> pdb=" O   PHE M 127 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 131 through 139
    Processing helix  chain 'M' and resid 140 through 143
      removed outlier: 3.662A  pdb=" N   LYS M 143 " --> pdb=" O   PRO M 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 140 through 143'
    Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13

    237 hydrogen bonds defined for protein.
    705 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: 0.37

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1078
        1.34 -     1.45: 470
        1.45 -     1.57: 1887
        1.57 -     1.69: 0
        1.69 -     1.80: 21
  Bond restraints: 3456
  Sorted by residual:
  bond pdb=" N   LEU M  76 "
       pdb=" CA  LEU M  76 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.25e-02 6.40e+03 6.36e+00
  bond pdb=" N   GLU K 178 "
       pdb=" CA  GLU K 178 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.20e-02 6.94e+03 6.19e+00
  bond pdb=" N   LYS K 168 "
       pdb=" CA  LYS K 168 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 4.89e+00
  bond pdb=" CB  PRO M 153 "
       pdb=" CG  PRO M 153 "
    ideal  model  delta    sigma   weight residual
    1.506  1.441  0.065 3.90e-02 6.57e+02 2.79e+00
  bond pdb=" CB  THR K 139 "
       pdb=" CG2 THR K 139 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  ... (remaining 3451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 4467
        1.92 -     3.84: 185
        3.84 -     5.77: 19
        5.77 -     7.69: 2
        7.69 -     9.61: 1
  Bond angle restraints: 4674
  Sorted by residual:
  angle pdb=" C   PHE K 125 "
        pdb=" N   ASP K 126 "
        pdb=" CA  ASP K 126 "
      ideal   model   delta    sigma   weight residual
     120.31  114.62    5.69 1.52e+00 4.33e-01 1.40e+01
  angle pdb=" C   LYS K  72 "
        pdb=" N   LYS K  73 "
        pdb=" CA  LYS K  73 "
      ideal   model   delta    sigma   weight residual
     121.80  114.95    6.85 2.16e+00 2.14e-01 1.01e+01
  angle pdb=" N   ARG K 121 "
        pdb=" CA  ARG K 121 "
        pdb=" C   ARG K 121 "
      ideal   model   delta    sigma   weight residual
     111.75  115.44   -3.69 1.28e+00 6.10e-01 8.31e+00
  angle pdb=" C   ILE K 174 "
        pdb=" N   ASN K 175 "
        pdb=" CA  ASN K 175 "
      ideal   model   delta    sigma   weight residual
     120.68  115.80    4.88 1.70e+00 3.46e-01 8.24e+00
  angle pdb=" CA  LEU K 117 "
        pdb=" CB  LEU K 117 "
        pdb=" CG  LEU K 117 "
      ideal   model   delta    sigma   weight residual
     116.30  125.91   -9.61 3.50e+00 8.16e-02 7.54e+00
  ... (remaining 4669 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.70: 1847
       16.70 -    33.39: 210
       33.39 -    50.09: 40
       50.09 -    66.79: 12
       66.79 -    83.49: 4
  Dihedral angle restraints: 2113
    sinusoidal: 862
      harmonic: 1251
  Sorted by residual:
  dihedral pdb=" CA  PHE L 100 "
           pdb=" C   PHE L 100 "
           pdb=" N   GLU L 101 "
           pdb=" CA  GLU L 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.42  -18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ILE M  10 "
           pdb=" C   ILE M  10 "
           pdb=" N   ASP M  11 "
           pdb=" CA  ASP M  11 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.47   18.53     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ARG K 121 "
           pdb=" C   ARG K 121 "
           pdb=" N   HIS K 122 "
           pdb=" CA  HIS K 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.52  -18.48     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 220
       0.029 -    0.058: 170
       0.058 -    0.087: 67
       0.087 -    0.116: 31
       0.116 -    0.145: 20
  Chirality restraints: 508
  Sorted by residual:
  chirality pdb=" CA  VAL M  80 "
            pdb=" N   VAL M  80 "
            pdb=" C   VAL M  80 "
            pdb=" CB  VAL M  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  PHE K  58 "
            pdb=" N   PHE K  58 "
            pdb=" C   PHE K  58 "
            pdb=" CB  PHE K  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.07e-01
  chirality pdb=" CA  PRO K  76 "
            pdb=" N   PRO K  76 "
            pdb=" C   PRO K  76 "
            pdb=" CB  PRO K  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 505 not shown)

  Planarity restraints: 603
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE M  69 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   PHE M  69 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PHE M  69 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLU M  70 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K 159 "   -0.009 2.00e-02 2.50e+03   1.78e-02 3.18e+00
        pdb=" C   ILE K 159 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE K 159 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER K 160 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE M 139 "    0.014 2.00e-02 2.50e+03   1.29e-02 2.90e+00
        pdb=" CG  PHE M 139 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE M 139 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE M 139 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE M 139 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE M 139 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE M 139 "    0.002 2.00e-02 2.50e+03
  ... (remaining 600 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 295
        2.72 -     3.27: 3535
        3.27 -     3.81: 5368
        3.81 -     4.36: 5909
        4.36 -     4.90: 10125
  Nonbonded interactions: 25232
  Sorted by model distance:
  nonbonded pdb=" O   VAL K 181 "
            pdb=" OG  SER K 184 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" NZ  LYS K  84 "
            pdb=" OE1 GLU K  87 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" NH1 ARG K 154 "
            pdb=" O   THR L  89 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OG1 THR L  56 "
            pdb=" O   GLY L  59 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OD1 ASP K 126 "
            pdb=" NH2 ARG K 129 "
     model   vdw
     2.278 3.120
  ... (remaining 25227 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:             9.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.360
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
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      :  0.007   0.065   3456  Z= 0.317
  Angle     :  0.878   9.610   4674  Z= 0.496
  Chirality :  0.052   0.145    508
  Planarity :  0.006   0.040    603
  Dihedral  : 15.253  83.485   1299
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.28 (0.34), residues: 413
  helix: -1.09 (0.25), residues: 285
  sheet:  None (None), residues: 0
  loop : -2.19 (0.51), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG M  40 
 TYR   0.020   0.003   TYR K 140 
 PHE   0.030   0.003   PHE M 139 
 TRP   0.024   0.004   TRP K 176 
 HIS   0.006   0.003   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00702 ( 3456)
  covalent geometry    : angle       0.87768 ( 4674)
  hydrogen bonds       : bond        0.11435 (  237)
  hydrogen bonds       : angle       5.11292 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   56 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7139 (tt0)
REVERT: K  154 ARG cc_start: 0.7546 (mtt-85) cc_final: 0.7256 (mtp180)
REVERT: K  169 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8248 (tp30)
REVERT: L   47 ILE cc_start: 0.8384 (pt) cc_final: 0.7695 (pt)
REVERT: L   91 PRO cc_start: 0.7630 (Cg_endo) cc_final: 0.7350 (Cg_exo)
REVERT: L  103 ILE cc_start: 0.5678 (mt) cc_final: 0.5461 (mt)
REVERT: L  105 LYS cc_start: 0.5593 (tmtt) cc_final: 0.5125 (tptt)
REVERT: M   96 ASP cc_start: 0.8088 (t0) cc_final: 0.7866 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0973
  time to fit residues: 13.0562
Evaluate side-chains
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0770
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0060
   overall best weight:    0.8158

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

Flipped N/Q/H residues before XYZ refinement:
K  88 GLN
K  98 GLN
K 115 GLN
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 183 GLN
** M  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  47 ASN
M  59 ASN
M 136 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.137520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.118285 restraints weight = 8162.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.119669 restraints weight = 4074.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.120981 restraints weight = 2039.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.120882 restraints weight = 1687.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.120981 restraints weight = 1446.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3456  Z= 0.146
  Angle     :  0.608   7.815   4674  Z= 0.327
  Chirality :  0.040   0.141    508
  Planarity :  0.005   0.045    603
  Dihedral  :  5.127  48.306    452
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 13.24 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.50 (0.41), residues: 413
  helix:  1.25 (0.30), residues: 286
  sheet:  None (None), residues: 0
  loop : -1.81 (0.55), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 154 
 TYR   0.021   0.002   TYR M  56 
 PHE   0.017   0.002   PHE L  93 
 TRP   0.017   0.002   TRP M  53 
 HIS   0.004   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3456)
  covalent geometry    : angle       0.60788 ( 4674)
  hydrogen bonds       : bond        0.05387 (  237)
  hydrogen bonds       : angle       4.22758 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  178 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7035 (tm-30)
REVERT: L   47 ILE cc_start: 0.8249 (pt) cc_final: 0.7650 (pt)
REVERT: L  103 ILE cc_start: 0.5785 (mt) cc_final: 0.5466 (mt)
REVERT: M  119 GLU cc_start: 0.6477 (tp30) cc_final: 0.6234 (tp30)
  outliers start: 14
  outliers final: 10
  residues processed: 92
  average time/residue: 0.0798
  time to fit residues: 8.6559
Evaluate side-chains
  79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  100 SER
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  161 VAL
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   93 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.135850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.116963 restraints weight = 8259.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.117894 restraints weight = 4269.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.119416 restraints weight = 2359.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.119268 restraints weight = 1802.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.119383 restraints weight = 1550.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3456  Z= 0.171
  Angle     :  0.608   6.943   4674  Z= 0.327
  Chirality :  0.041   0.146    508
  Planarity :  0.005   0.046    603
  Dihedral  :  4.827  39.765    452
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 17.46 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.34 (0.42), residues: 413
  helix:  1.87 (0.30), residues: 286
  sheet:  None (None), residues: 0
  loop : -1.45 (0.58), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 167 
 TYR   0.014   0.002   TYR K  74 
 PHE   0.020   0.002   PHE K  24 
 TRP   0.017   0.002   TRP M  53 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3456)
  covalent geometry    : angle       0.60803 ( 4674)
  hydrogen bonds       : bond        0.05201 (  237)
  hydrogen bonds       : angle       4.21455 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: K  148 TYR cc_start: 0.7873 (t80) cc_final: 0.7529 (t80)
REVERT: K  169 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8369 (tp30)
REVERT: L   47 ILE cc_start: 0.8256 (pt) cc_final: 0.7723 (pt)
REVERT: M   92 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6663 (tp30)
REVERT: M  119 GLU cc_start: 0.6556 (tp30) cc_final: 0.6299 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 0.0793
  time to fit residues: 8.2821
Evaluate side-chains
  82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 LYS
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  161 VAL
Chi-restraints excluded: chain K residue  169 GLU
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   92 GLU
Chi-restraints excluded: chain M residue   93 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 11 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.137891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.119011 restraints weight = 8153.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.120684 restraints weight = 3784.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121262 restraints weight = 2168.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121380 restraints weight = 1944.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.121485 restraints weight = 1592.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3456  Z= 0.132
  Angle     :  0.565   6.350   4674  Z= 0.306
  Chirality :  0.039   0.139    508
  Planarity :  0.005   0.043    603
  Dihedral  :  4.596  33.522    452
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.72 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.90 (0.43), residues: 413
  helix:  2.38 (0.30), residues: 279
  sheet:  None (None), residues: 0
  loop : -1.27 (0.56), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 154 
 TYR   0.017   0.001   TYR M  85 
 PHE   0.027   0.002   PHE K  24 
 TRP   0.024   0.002   TRP M  53 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3456)
  covalent geometry    : angle       0.56521 ( 4674)
  hydrogen bonds       : bond        0.05025 (  237)
  hydrogen bonds       : angle       4.05596 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  148 TYR cc_start: 0.7812 (t80) cc_final: 0.7403 (t80)
REVERT: K  165 MET cc_start: 0.8300 (mtp) cc_final: 0.6963 (tmm)
REVERT: K  178 GLU cc_start: 0.7986 (mm-30) cc_final: 0.6899 (tm-30)
REVERT: L   47 ILE cc_start: 0.8224 (pt) cc_final: 0.7691 (pt)
REVERT: L   81 MET cc_start: 0.8271 (ppp) cc_final: 0.7773 (ppp)
REVERT: M   92 GLU cc_start: 0.6955 (tp30) cc_final: 0.6622 (tp30)
REVERT: M  119 GLU cc_start: 0.6572 (tp30) cc_final: 0.6340 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0829
  time to fit residues: 8.2948
Evaluate side-chains
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   23 GLN
Chi-restraints excluded: chain M residue   93 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 26 optimal weight:    0.0170
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 180 HIS
** M  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.137638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.118796 restraints weight = 8277.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.120607 restraints weight = 3702.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121281 restraints weight = 2147.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121210 restraints weight = 1823.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.121375 restraints weight = 1669.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3456  Z= 0.129
  Angle     :  0.568   5.590   4674  Z= 0.309
  Chirality :  0.039   0.138    508
  Planarity :  0.005   0.041    603
  Dihedral  :  4.386  27.658    452
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.72 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.24 (0.42), residues: 413
  helix:  2.54 (0.30), residues: 282
  sheet:  None (None), residues: 0
  loop : -0.97 (0.58), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG M  40 
 TYR   0.010   0.001   TYR K  74 
 PHE   0.020   0.002   PHE K  24 
 TRP   0.011   0.001   TRP M  53 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3456)
  covalent geometry    : angle       0.56820 ( 4674)
  hydrogen bonds       : bond        0.04923 (  237)
  hydrogen bonds       : angle       3.96887 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: K  148 TYR cc_start: 0.7819 (t80) cc_final: 0.7359 (t80)
REVERT: K  165 MET cc_start: 0.8302 (mtp) cc_final: 0.7009 (tmm)
REVERT: L   47 ILE cc_start: 0.8207 (pt) cc_final: 0.7752 (pt)
REVERT: M   92 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6598 (tp30)
REVERT: M  119 GLU cc_start: 0.6669 (tp30) cc_final: 0.6463 (tp30)
  outliers start: 12
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0878
  time to fit residues: 8.5812
Evaluate side-chains
  80 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 LYS
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   92 GLU
Chi-restraints excluded: chain M residue   93 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.3980
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 38 optimal weight:    0.1980
   chunk 27 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
K 128 GLN
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 180 HIS
** M  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.138028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.119603 restraints weight = 8235.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.120781 restraints weight = 3586.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121565 restraints weight = 2300.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.121659 restraints weight = 1950.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.121763 restraints weight = 1619.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3456  Z= 0.126
  Angle     :  0.568   7.884   4674  Z= 0.305
  Chirality :  0.039   0.138    508
  Planarity :  0.005   0.052    603
  Dihedral  :  4.168  21.442    452
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.28 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.46 (0.42), residues: 413
  helix:  2.71 (0.29), residues: 284
  sheet:  None (None), residues: 0
  loop : -0.95 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 154 
 TYR   0.007   0.001   TYR K 157 
 PHE   0.010   0.001   PHE L 100 
 TRP   0.007   0.001   TRP M  53 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3456)
  covalent geometry    : angle       0.56756 ( 4674)
  hydrogen bonds       : bond        0.04803 (  237)
  hydrogen bonds       : angle       3.90284 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: K  148 TYR cc_start: 0.7778 (t80) cc_final: 0.7214 (t80)
REVERT: K  165 MET cc_start: 0.8300 (mtp) cc_final: 0.6961 (tmm)
REVERT: L   47 ILE cc_start: 0.8207 (pt) cc_final: 0.7767 (pt)
REVERT: L   81 MET cc_start: 0.8225 (ppp) cc_final: 0.7905 (tmm)
REVERT: L  101 GLU cc_start: 0.5647 (mp0) cc_final: 0.5377 (mp0)
REVERT: M   92 GLU cc_start: 0.6940 (tp30) cc_final: 0.6565 (tp30)
REVERT: M  119 GLU cc_start: 0.6648 (tp30) cc_final: 0.6443 (tp30)
REVERT: M  157 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7053 (mp)
  outliers start: 13
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0866
  time to fit residues: 8.3026
Evaluate side-chains
  79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 LYS
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  180 HIS
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   93 GLU
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
K 128 GLN
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 180 HIS
L  40 GLN
** M  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.137706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.119127 restraints weight = 8465.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.119680 restraints weight = 5030.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121335 restraints weight = 2787.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121293 restraints weight = 1856.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.121456 restraints weight = 1671.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3456  Z= 0.136
  Angle     :  0.623   7.586   4674  Z= 0.330
  Chirality :  0.041   0.210    508
  Planarity :  0.005   0.050    603
  Dihedral  :  4.093  18.423    452
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 21.41 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.50 (0.42), residues: 413
  helix:  2.71 (0.29), residues: 285
  sheet:  None (None), residues: 0
  loop : -0.88 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 166 
 TYR   0.006   0.001   TYR M  85 
 PHE   0.021   0.002   PHE K  24 
 TRP   0.008   0.001   TRP M  53 
 HIS   0.004   0.001   HIS K 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3456)
  covalent geometry    : angle       0.62261 ( 4674)
  hydrogen bonds       : bond        0.04791 (  237)
  hydrogen bonds       : angle       3.95252 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  148 TYR cc_start: 0.7757 (t80) cc_final: 0.7209 (t80)
REVERT: K  165 MET cc_start: 0.8265 (mtp) cc_final: 0.6933 (tmm)
REVERT: L   47 ILE cc_start: 0.8169 (pt) cc_final: 0.7779 (pt)
REVERT: L  101 GLU cc_start: 0.5599 (mp0) cc_final: 0.5389 (mp0)
REVERT: M   92 GLU cc_start: 0.6846 (tp30) cc_final: 0.6496 (tp30)
REVERT: M  119 GLU cc_start: 0.6771 (tp30) cc_final: 0.6542 (tp30)
REVERT: M  157 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7030 (mp)
  outliers start: 13
  outliers final: 10
  residues processed: 80
  average time/residue: 0.0780
  time to fit residues: 7.4266
Evaluate side-chains
  82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 LYS
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  180 HIS
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   19 ILE
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0030
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 180 HIS
L  40 GLN
** L  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.138102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.119379 restraints weight = 8335.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.120417 restraints weight = 4754.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.121170 restraints weight = 2977.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.121354 restraints weight = 2131.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121542 restraints weight = 1853.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3456  Z= 0.135
  Angle     :  0.628   7.383   4674  Z= 0.333
  Chirality :  0.041   0.202    508
  Planarity :  0.005   0.048    603
  Dihedral  :  4.047  19.071    452
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.82 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.59 (0.42), residues: 413
  helix:  2.77 (0.29), residues: 285
  sheet:  None (None), residues: 0
  loop : -0.83 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 166 
 TYR   0.006   0.001   TYR L  50 
 PHE   0.027   0.002   PHE K 125 
 TRP   0.008   0.001   TRP K 176 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3456)
  covalent geometry    : angle       0.62801 ( 4674)
  hydrogen bonds       : bond        0.04720 (  237)
  hydrogen bonds       : angle       3.92355 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.088 
Fit side-chains
REVERT: K  120 LYS cc_start: 0.8601 (tppt) cc_final: 0.7953 (ttpt)
REVERT: K  148 TYR cc_start: 0.7749 (t80) cc_final: 0.7230 (t80)
REVERT: K  165 MET cc_start: 0.8227 (mtp) cc_final: 0.6972 (tmm)
REVERT: L   47 ILE cc_start: 0.8150 (pt) cc_final: 0.7893 (pt)
REVERT: L   55 GLN cc_start: 0.7722 (pp30) cc_final: 0.7457 (pp30)
REVERT: M   92 GLU cc_start: 0.6821 (tp30) cc_final: 0.6467 (tp30)
REVERT: M  157 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7025 (mp)
  outliers start: 12
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0703
  time to fit residues: 6.7252
Evaluate side-chains
  78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 LYS
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   19 ILE
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0040
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  40 GLN
** L  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.138855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.120230 restraints weight = 8384.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.121522 restraints weight = 4000.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.122632 restraints weight = 2285.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.122537 restraints weight = 2038.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.122627 restraints weight = 1657.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3456  Z= 0.133
  Angle     :  0.629   6.702   4674  Z= 0.334
  Chirality :  0.041   0.198    508
  Planarity :  0.005   0.047    603
  Dihedral  :  3.970  19.133    452
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 23.94 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.66 (0.42), residues: 413
  helix:  2.80 (0.29), residues: 285
  sheet:  None (None), residues: 0
  loop : -0.76 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 166 
 TYR   0.007   0.001   TYR L  50 
 PHE   0.023   0.002   PHE K  24 
 TRP   0.017   0.001   TRP K 176 
 HIS   0.004   0.001   HIS K 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3456)
  covalent geometry    : angle       0.62896 ( 4674)
  hydrogen bonds       : bond        0.04679 (  237)
  hydrogen bonds       : angle       3.90590 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: K  120 LYS cc_start: 0.8598 (tppt) cc_final: 0.7977 (ttpt)
REVERT: K  148 TYR cc_start: 0.7744 (t80) cc_final: 0.7220 (t80)
REVERT: K  165 MET cc_start: 0.8234 (mtp) cc_final: 0.6918 (tmm)
REVERT: L   50 TYR cc_start: 0.2885 (t80) cc_final: 0.2601 (t80)
REVERT: L   55 GLN cc_start: 0.7702 (pp30) cc_final: 0.7466 (pp30)
REVERT: M   92 GLU cc_start: 0.6732 (tp30) cc_final: 0.6366 (tp30)
REVERT: M  157 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7068 (mp)
  outliers start: 11
  outliers final: 9
  residues processed: 77
  average time/residue: 0.0803
  time to fit residues: 7.1549
Evaluate side-chains
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 LYS
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   19 ILE
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0470
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.8480

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

Flipped N/Q/H residues before XYZ refinement:
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.138478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.119808 restraints weight = 8336.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.121227 restraints weight = 3852.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121666 restraints weight = 2493.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.121782 restraints weight = 2153.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.121891 restraints weight = 1818.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.4600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3456  Z= 0.141
  Angle     :  0.656   9.500   4674  Z= 0.350
  Chirality :  0.041   0.188    508
  Planarity :  0.005   0.047    603
  Dihedral  :  3.994  19.413    452
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 24.51 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.57 (0.42), residues: 413
  helix:  2.72 (0.29), residues: 285
  sheet:  None (None), residues: 0
  loop : -0.76 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 166 
 TYR   0.006   0.001   TYR L  50 
 PHE   0.012   0.001   PHE K 125 
 TRP   0.019   0.003   TRP M  53 
 HIS   0.004   0.001   HIS K 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3456)
  covalent geometry    : angle       0.65634 ( 4674)
  hydrogen bonds       : bond        0.04672 (  237)
  hydrogen bonds       : angle       3.94122 (  705)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.089 
Fit side-chains
REVERT: K  120 LYS cc_start: 0.8593 (tppt) cc_final: 0.7957 (ttpt)
REVERT: K  148 TYR cc_start: 0.7754 (t80) cc_final: 0.7252 (t80)
REVERT: K  165 MET cc_start: 0.8202 (mtp) cc_final: 0.6990 (tmm)
REVERT: L   50 TYR cc_start: 0.2885 (t80) cc_final: 0.2576 (t80)
REVERT: M   92 GLU cc_start: 0.6736 (tp30) cc_final: 0.6366 (tp30)
REVERT: M  157 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7044 (mp)
  outliers start: 12
  outliers final: 10
  residues processed: 71
  average time/residue: 0.0716
  time to fit residues: 6.0887
Evaluate side-chains
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 LYS
Chi-restraints excluded: chain K residue   67 MET
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  180 HIS
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   74 GLU
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   19 ILE
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0170
   chunk 36 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.138497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.120216 restraints weight = 8442.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.121990 restraints weight = 4944.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.122125 restraints weight = 3546.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.122608 restraints weight = 2713.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.122571 restraints weight = 2615.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3456  Z= 0.141
  Angle     :  0.684   7.947   4674  Z= 0.364
  Chirality :  0.041   0.189    508
  Planarity :  0.005   0.047    603
  Dihedral  :  4.015  19.639    452
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 25.92 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.50 (0.42), residues: 413
  helix:  2.68 (0.29), residues: 285
  sheet:  None (None), residues: 0
  loop : -0.81 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 167 
 TYR   0.006   0.001   TYR L  50 
 PHE   0.023   0.002   PHE K  24 
 TRP   0.018   0.002   TRP M  12 
 HIS   0.004   0.001   HIS K 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3456)
  covalent geometry    : angle       0.68441 ( 4674)
  hydrogen bonds       : bond        0.04728 (  237)
  hydrogen bonds       : angle       3.93849 (  705)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1131.75 seconds
wall clock time: 20 minutes 6.07 seconds (1206.07 seconds total)