Starting phenix.real_space_refine
on Wed Jul 23 13:30:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h9n_34574/07_2025/8h9n_34574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h9n_34574/07_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_34574/07_2025/8h9n_34574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h9n_34574/07_2025/8h9n_34574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h9n_34574/07_2025/8h9n_34574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h9n_34574/07_2025/8h9n_34574.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.84, per 1000 atoms: 1.43
  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: 0.87
  Conformation dependent library (CDL) restraints added in 406.8 milliseconds
  

  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: 0.29
  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: 0.83

  Time building geometry restraints manager: 1.03 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:             10.330
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.220
  Find NCS groups from input model:        0.040
  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:3.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.580
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (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
 TRP   0.024   0.004   TRP K 176 
 HIS   0.006   0.003   HIS K 158 
 PHE   0.030   0.003   PHE M 139 
 TYR   0.020   0.003   TYR K 140 
 ARG   0.004   0.001   ARG M  40 

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

*********************** 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  : 0.430 
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: 0.3185
  time to fit residues: 43.0052
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  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 103 HIS
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.135888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.117598 restraints weight = 8191.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.118685 restraints weight = 4599.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.119181 restraints weight = 3622.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3456  Z= 0.170
  Angle     :  0.628   7.622   4674  Z= 0.340
  Chirality :  0.041   0.145    508
  Planarity :  0.006   0.046    603
  Dihedral  :  5.153  45.988    452
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 14.65 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.41), residues: 413
  helix:  1.19 (0.30), residues: 286
  sheet:  None (None), residues: 0
  loop : -1.80 (0.56), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP M  53 
 HIS   0.003   0.002   HIS K 103 
 PHE   0.018   0.002   PHE L  93 
 TYR   0.019   0.002   TYR K  74 
 ARG   0.006   0.001   ARG K 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05457 (  237)
  hydrogen bonds       : angle       4.32315 (  705)
  covalent geometry    : bond        0.00369 ( 3456)
  covalent geometry    : angle       0.62782 ( 4674)

*********************** 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
  101 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  154 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.6964 (ttm170)
REVERT: L  103 ILE cc_start: 0.5918 (mt) cc_final: 0.5502 (mt)
REVERT: M   96 ASP cc_start: 0.7958 (t0) cc_final: 0.7749 (t70)
REVERT: M  119 GLU cc_start: 0.6536 (tp30) cc_final: 0.6320 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1836
  time to fit residues: 20.3619
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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 12 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 37 optimal weight:    0.1980
   chunk 16 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**
M  23 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.136919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.119163 restraints weight = 8109.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.119352 restraints weight = 3338.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.120033 restraints weight = 2495.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3456  Z= 0.133
  Angle     :  0.573   7.167   4674  Z= 0.309
  Chirality :  0.039   0.141    508
  Planarity :  0.005   0.043    603
  Dihedral  :  4.778  39.484    452
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 18.59 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.43), residues: 413
  helix:  1.99 (0.30), residues: 285
  sheet:  None (None), residues: 0
  loop : -1.45 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP M  53 
 HIS   0.002   0.001   HIS K 158 
 PHE   0.021   0.002   PHE K  24 
 TYR   0.017   0.002   TYR K  74 
 ARG   0.006   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05090 (  237)
  hydrogen bonds       : angle       4.16038 (  705)
  covalent geometry    : bond        0.00269 ( 3456)
  covalent geometry    : angle       0.57281 ( 4674)

*********************** 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
  97 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  169 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8279 (tp30)
REVERT: K  178 GLU cc_start: 0.8036 (mm-30) cc_final: 0.6875 (tm-30)
REVERT: L   80 GLN cc_start: 0.8299 (pp30) cc_final: 0.8088 (pt0)
REVERT: L   81 MET cc_start: 0.8295 (ppp) cc_final: 0.8002 (ppp)
REVERT: M   92 GLU cc_start: 0.6821 (tp30) cc_final: 0.6491 (tp30)
REVERT: M   96 ASP cc_start: 0.7926 (t0) cc_final: 0.7682 (t70)
REVERT: M  119 GLU cc_start: 0.6535 (tp30) cc_final: 0.6305 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 90
  average time/residue: 0.2873
  time to fit residues: 31.2549
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 2.511 
-------------------------------------------------------------------------------
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  147 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   93 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.136350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.114824 restraints weight = 8243.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.117020 restraints weight = 3897.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.118339 restraints weight = 2319.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3456  Z= 0.158
  Angle     :  0.579   5.651   4674  Z= 0.315
  Chirality :  0.040   0.150    508
  Planarity :  0.005   0.044    603
  Dihedral  :  4.585  32.449    452
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 20.00 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.43), residues: 413
  helix:  2.12 (0.30), residues: 286
  sheet:  None (None), residues: 0
  loop : -1.36 (0.58), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP M  53 
 HIS   0.002   0.001   HIS K 158 
 PHE   0.026   0.002   PHE K  24 
 TYR   0.012   0.002   TYR M  85 
 ARG   0.006   0.001   ARG K 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05067 (  237)
  hydrogen bonds       : angle       4.13847 (  705)
  covalent geometry    : bond        0.00340 ( 3456)
  covalent geometry    : angle       0.57883 ( 4674)

*********************** 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
  87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  154 ARG cc_start: 0.7165 (mtp180) cc_final: 0.6594 (mtt180)
REVERT: K  164 MET cc_start: 0.8438 (tpt) cc_final: 0.8160 (tpt)
REVERT: K  165 MET cc_start: 0.8290 (mtp) cc_final: 0.6907 (tmm)
REVERT: K  178 GLU cc_start: 0.8019 (mm-30) cc_final: 0.6950 (tm-30)
REVERT: M   92 GLU cc_start: 0.6967 (tp30) cc_final: 0.6635 (tp30)
REVERT: M   96 ASP cc_start: 0.7912 (t0) cc_final: 0.7670 (t70)
REVERT: M  119 GLU cc_start: 0.6643 (tp30) cc_final: 0.6392 (tp30)
  outliers start: 15
  outliers final: 13
  residues processed: 79
  average time/residue: 0.2485
  time to fit residues: 23.5661
Evaluate side-chains
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
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  147 VAL
Chi-restraints excluded: chain K residue  161 VAL
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 L residue   97 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 28 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0370
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.1862

-------------------------------------------------------------------------------
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 ** 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 = 0.4017 r_free = 0.4017 target = 0.136331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.118189 restraints weight = 8198.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.119449 restraints weight = 4691.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.119946 restraints weight = 3278.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3456  Z= 0.146
  Angle     :  0.578   7.576   4674  Z= 0.312
  Chirality :  0.040   0.138    508
  Planarity :  0.005   0.043    603
  Dihedral  :  4.387  25.844    452
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 20.56 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.42), residues: 413
  helix:  2.40 (0.30), residues: 280
  sheet:  None (None), residues: 0
  loop : -1.16 (0.56), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP M  53 
 HIS   0.002   0.001   HIS K 180 
 PHE   0.019   0.002   PHE K  24 
 TYR   0.026   0.002   TYR M  85 
 ARG   0.004   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04981 (  237)
  hydrogen bonds       : angle       4.05137 (  705)
  covalent geometry    : bond        0.00309 ( 3456)
  covalent geometry    : angle       0.57754 ( 4674)

*********************** 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
  86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  154 ARG cc_start: 0.7153 (mtp180) cc_final: 0.6643 (mtt180)
REVERT: K  165 MET cc_start: 0.8302 (mtp) cc_final: 0.6993 (tmm)
REVERT: K  178 GLU cc_start: 0.7883 (mm-30) cc_final: 0.6911 (tm-30)
REVERT: M   92 GLU cc_start: 0.6985 (tp30) cc_final: 0.6647 (tp30)
REVERT: M   96 ASP cc_start: 0.7957 (t0) cc_final: 0.7616 (t0)
REVERT: M  119 GLU cc_start: 0.6647 (tp30) cc_final: 0.6392 (tp30)
REVERT: M  157 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7095 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 77
  average time/residue: 0.1821
  time to fit residues: 16.7032
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  : 0.384 
-------------------------------------------------------------------------------
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  147 VAL
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 L residue   97 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 35 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 ** 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 = 0.4018 r_free = 0.4018 target = 0.136452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.116879 restraints weight = 8423.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.117964 restraints weight = 3967.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.118052 restraints weight = 2982.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3456  Z= 0.138
  Angle     :  0.577   6.725   4674  Z= 0.310
  Chirality :  0.039   0.138    508
  Planarity :  0.005   0.042    603
  Dihedral  :  4.198  19.364    452
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 18.87 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.42), residues: 413
  helix:  2.56 (0.30), residues: 280
  sheet:  None (None), residues: 0
  loop : -1.06 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP M  53 
 HIS   0.001   0.001   HIS K 158 
 PHE   0.017   0.002   PHE K  24 
 TYR   0.025   0.002   TYR M  85 
 ARG   0.003   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04906 (  237)
  hydrogen bonds       : angle       4.02114 (  705)
  covalent geometry    : bond        0.00286 ( 3456)
  covalent geometry    : angle       0.57730 ( 4674)

*********************** 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: 17
    poor density    : 71
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: K  154 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6642 (ttm170)
REVERT: K  164 MET cc_start: 0.8444 (tpp) cc_final: 0.8195 (tpp)
REVERT: K  165 MET cc_start: 0.8278 (mtp) cc_final: 0.6977 (tmm)
REVERT: K  178 GLU cc_start: 0.8052 (mm-30) cc_final: 0.6901 (tm-30)
REVERT: L   80 GLN cc_start: 0.8331 (pp30) cc_final: 0.8130 (pt0)
REVERT: L   81 MET cc_start: 0.8450 (ppp) cc_final: 0.8149 (ppp)
REVERT: M   92 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6738 (tp30)
REVERT: M   96 ASP cc_start: 0.8084 (t0) cc_final: 0.7789 (t70)
REVERT: M  119 GLU cc_start: 0.6774 (tp30) cc_final: 0.6545 (tp30)
REVERT: M  157 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7070 (mp)
  outliers start: 17
  outliers final: 12
  residues processed: 80
  average time/residue: 0.1863
  time to fit residues: 17.6356
Evaluate side-chains
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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  182 VAL
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain M residue   13 VAL
Chi-restraints excluded: chain M residue   80 VAL
Chi-restraints excluded: chain M residue   92 GLU
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 15 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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
** 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 = 0.4019 r_free = 0.4019 target = 0.136479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.117627 restraints weight = 8278.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.118836 restraints weight = 4299.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.120019 restraints weight = 2251.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3456  Z= 0.144
  Angle     :  0.597   7.882   4674  Z= 0.323
  Chirality :  0.040   0.138    508
  Planarity :  0.005   0.041    603
  Dihedral  :  4.069  17.476    452
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.28 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.42), residues: 413
  helix:  2.60 (0.30), residues: 280
  sheet:  None (None), residues: 0
  loop : -1.01 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP M  53 
 HIS   0.002   0.001   HIS K 172 
 PHE   0.016   0.002   PHE K  24 
 TYR   0.022   0.002   TYR M  85 
 ARG   0.004   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04834 (  237)
  hydrogen bonds       : angle       3.98837 (  705)
  covalent geometry    : bond        0.00305 ( 3456)
  covalent geometry    : angle       0.59683 ( 4674)

*********************** 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: 19
    poor density    : 69
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  154 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6672 (ttm170)
REVERT: K  165 MET cc_start: 0.8227 (mtp) cc_final: 0.6957 (tmm)
REVERT: K  178 GLU cc_start: 0.7884 (mm-30) cc_final: 0.6949 (tm-30)
REVERT: L  101 GLU cc_start: 0.5593 (mp0) cc_final: 0.5295 (mp0)
REVERT: M   92 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6631 (tp30)
REVERT: M   96 ASP cc_start: 0.7945 (t0) cc_final: 0.7599 (t0)
REVERT: M  119 GLU cc_start: 0.6717 (tp30) cc_final: 0.6473 (tp30)
REVERT: M  157 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7115 (mp)
  outliers start: 19
  outliers final: 14
  residues processed: 80
  average time/residue: 0.1822
  time to fit residues: 17.3444
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
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  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   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   80 VAL
Chi-restraints excluded: chain M residue   92 GLU
Chi-restraints excluded: chain M residue   93 GLU
Chi-restraints excluded: chain M residue  125 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 25 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0270
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.3642

-------------------------------------------------------------------------------
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
** 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 = 0.4009 r_free = 0.4009 target = 0.135594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.116781 restraints weight = 8299.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.118490 restraints weight = 4098.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.119229 restraints weight = 2178.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3456  Z= 0.161
  Angle     :  0.661   6.630   4674  Z= 0.354
  Chirality :  0.042   0.179    508
  Planarity :  0.005   0.042    603
  Dihedral  :  4.139  18.192    452
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.42), residues: 413
  helix:  2.57 (0.30), residues: 280
  sheet:  None (None), residues: 0
  loop : -1.03 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP M  53 
 HIS   0.002   0.001   HIS K 172 
 PHE   0.010   0.002   PHE M 127 
 TYR   0.024   0.002   TYR M  85 
 ARG   0.007   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04916 (  237)
  hydrogen bonds       : angle       4.00097 (  705)
  covalent geometry    : bond        0.00358 ( 3456)
  covalent geometry    : angle       0.66102 ( 4674)

*********************** 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: 19
    poor density    : 68
  time to evaluate  : 0.743 
Fit side-chains
REVERT: K  120 LYS cc_start: 0.8731 (tppt) cc_final: 0.8141 (ttpt)
REVERT: K  154 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6683 (ttm170)
REVERT: K  165 MET cc_start: 0.8241 (mtp) cc_final: 0.6950 (tmm)
REVERT: L   55 GLN cc_start: 0.7755 (pp30) cc_final: 0.7456 (pp30)
REVERT: M   92 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6678 (tp30)
REVERT: M   96 ASP cc_start: 0.7971 (t0) cc_final: 0.7691 (t70)
REVERT: M  119 GLU cc_start: 0.6720 (tp30) cc_final: 0.6467 (tp30)
REVERT: M  157 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7115 (mp)
  outliers start: 19
  outliers final: 14
  residues processed: 79
  average time/residue: 0.2953
  time to fit residues: 27.5034
Evaluate side-chains
  78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
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  104 ILE
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  161 VAL
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   80 VAL
Chi-restraints excluded: chain M residue   92 GLU
Chi-restraints excluded: chain M residue   93 GLU
Chi-restraints excluded: chain M residue  125 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 27 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0040
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 28 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.8796

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

Flipped N/Q/H residues before XYZ refinement:
K 130 ASN
** 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 = 0.4026 r_free = 0.4026 target = 0.136920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.118448 restraints weight = 8165.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.119792 restraints weight = 3708.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.120509 restraints weight = 2215.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3456  Z= 0.141
  Angle     :  0.657   7.513   4674  Z= 0.345
  Chirality :  0.041   0.158    508
  Planarity :  0.005   0.040    603
  Dihedral  :  4.087  19.102    452
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 24.23 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.42), residues: 413
  helix:  2.74 (0.30), residues: 280
  sheet:  None (None), residues: 0
  loop : -0.97 (0.56), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP M  53 
 HIS   0.003   0.001   HIS K 180 
 PHE   0.023   0.001   PHE K  24 
 TYR   0.024   0.001   TYR K 148 
 ARG   0.006   0.001   ARG L  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04800 (  237)
  hydrogen bonds       : angle       3.91560 (  705)
  covalent geometry    : bond        0.00301 ( 3456)
  covalent geometry    : angle       0.65708 ( 4674)

*********************** 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
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.660 
Fit side-chains
REVERT: K  120 LYS cc_start: 0.8728 (tppt) cc_final: 0.8094 (ttpt)
REVERT: K  154 ARG cc_start: 0.7037 (mtp180) cc_final: 0.6508 (mtt180)
REVERT: K  165 MET cc_start: 0.8224 (mtp) cc_final: 0.6930 (tmm)
REVERT: M   92 GLU cc_start: 0.6984 (tp30) cc_final: 0.6612 (tp30)
REVERT: M  119 GLU cc_start: 0.6720 (tp30) cc_final: 0.6476 (tp30)
REVERT: M  157 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7067 (mp)
  outliers start: 11
  outliers final: 10
  residues processed: 72
  average time/residue: 0.3213
  time to fit residues: 27.6325
Evaluate side-chains
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
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 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   80 VAL
Chi-restraints excluded: chain M residue   93 GLU
Chi-restraints excluded: chain M residue  125 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 16 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0070
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1402

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

Flipped N/Q/H residues before XYZ refinement:
K 128 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 = 0.4017 r_free = 0.4017 target = 0.136369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.117627 restraints weight = 8172.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.119355 restraints weight = 3757.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.119674 restraints weight = 2314.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4506

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= 0.152
  Angle     :  0.672   6.945   4674  Z= 0.353
  Chirality :  0.042   0.227    508
  Planarity :  0.005   0.041    603
  Dihedral  :  4.134  19.410    452
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.92 %
    Favored  : 70.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.42), residues: 413
  helix:  2.68 (0.30), residues: 280
  sheet:  None (None), residues: 0
  loop : -0.98 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP M  53 
 HIS   0.002   0.001   HIS K 172 
 PHE   0.023   0.002   PHE K 125 
 TYR   0.025   0.001   TYR M  85 
 ARG   0.005   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04807 (  237)
  hydrogen bonds       : angle       3.96642 (  705)
  covalent geometry    : bond        0.00337 ( 3456)
  covalent geometry    : angle       0.67197 ( 4674)

********************** 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
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
REVERT: K  120 LYS cc_start: 0.8702 (tppt) cc_final: 0.8075 (ttpt)
REVERT: K  148 TYR cc_start: 0.7446 (t80) cc_final: 0.7205 (t80)
REVERT: K  154 ARG cc_start: 0.7042 (mtp180) cc_final: 0.6546 (mtt180)
REVERT: K  165 MET cc_start: 0.8212 (mtp) cc_final: 0.6946 (tmm)
REVERT: L   55 GLN cc_start: 0.7721 (pp30) cc_final: 0.7479 (pp30)
REVERT: M   92 GLU cc_start: 0.6922 (tp30) cc_final: 0.6565 (tp30)
REVERT: M  119 GLU cc_start: 0.6782 (tp30) cc_final: 0.6529 (tp30)
REVERT: M  157 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.6930 (mp)
  outliers start: 11
  outliers final: 10
  residues processed: 71
  average time/residue: 0.3899
  time to fit residues: 33.2464
Evaluate side-chains
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   67 MET
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  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   80 VAL
Chi-restraints excluded: chain M residue  125 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 9 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4022 r_free = 0.4022 target = 0.136809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.117874 restraints weight = 8304.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.119462 restraints weight = 3718.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.120326 restraints weight = 2127.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3456  Z= 0.152
  Angle     :  0.684   7.166   4674  Z= 0.359
  Chirality :  0.042   0.206    508
  Planarity :  0.005   0.041    603
  Dihedral  :  4.154  19.650    452
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 24.79 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.42), residues: 413
  helix:  2.69 (0.30), residues: 280
  sheet:  None (None), residues: 0
  loop : -0.97 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP M  53 
 HIS   0.001   0.001   HIS K 158 
 PHE   0.021   0.002   PHE K  24 
 TYR   0.024   0.001   TYR M  85 
 ARG   0.005   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04829 (  237)
  hydrogen bonds       : angle       3.98395 (  705)
  covalent geometry    : bond        0.00337 ( 3456)
  covalent geometry    : angle       0.68385 ( 4674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3244.85 seconds
wall clock time: 61 minutes 6.72 seconds (3666.72 seconds total)