Starting phenix.real_space_refine
on Sat Apr 26 18:16:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5lii_4053/04_2025/5lii_4053.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5lii_4053/04_2025/5lii_4053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5lii_4053/04_2025/5lii_4053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5lii_4053/04_2025/5lii_4053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5lii_4053/04_2025/5lii_4053.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5lii_4053/04_2025/5lii_4053.cif"
  }
  resolution = 3.8
  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=   0.270
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    1947      2.51       5
     N     545      2.21       5
     O     595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3098
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "P"
      Number of atoms: 3098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3098
          Classifications: {'peptide': 433}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 414}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 273
          Unresolved non-hydrogen angles: 350
          Unresolved non-hydrogen dihedrals: 215
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 154
  Time building chain proxies: 2.39, per 1000 atoms: 0.77
  Number of scatterers: 3098
  At special positions: 0
  Unit cell: (66.24, 100.74, 97.98, 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     595      8.00
     N     545      7.00
     C    1947      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: 0.82
  Conformation dependent library (CDL) restraints added in 419.8 milliseconds
  

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  806

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 5 sheets defined
      11.5% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'P' and resid 63 through 68
    Processing helix  chain 'P' and resid 125 through 131
    Processing helix  chain 'P' and resid 137 through 159
      removed outlier: 3.620A  pdb=" N   THR P 142 " --> pdb=" O   SER P 138 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLU P 154 " --> pdb=" O   ALA P 150 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR P 159 " --> pdb=" O   TRP P 155 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 197 through 210
      removed outlier: 3.528A  pdb=" N   ASN P 201 " --> pdb=" O   GLU P 197 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY P 210 " --> pdb=" O   ARG P 206 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'P' and resid 70 through 72
      removed outlier: 6.829A  pdb=" N   ARG P  71 " --> pdb=" O   GLU P 418 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 82 through 84
    Processing sheet with id=AA3, first strand: chain 'P' and resid 325 through 326
      removed outlier: 3.509A  pdb=" N   SER P 326 " --> pdb=" O   ILE P 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'P' and resid 348 through 350
    Processing sheet with id=AA5, first strand: chain 'P' and resid 404 through 407

    41 hydrogen bonds defined for protein.
    114 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: 0.61

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 542
        1.27 -     1.41: 749
        1.41 -     1.55: 1832
        1.55 -     1.69: 3
        1.69 -     1.83: 22
  Bond restraints: 3148
  Sorted by residual:
  bond pdb=" C   ALA P 101 "
       pdb=" N   PRO P 102 "
    ideal  model  delta    sigma   weight residual
    1.334  1.134  0.200 2.34e-02 1.83e+03 7.32e+01
  bond pdb=" CA  MET P 409 "
       pdb=" CB  MET P 409 "
    ideal  model  delta    sigma   weight residual
    1.528  1.420  0.109 1.35e-02 5.49e+03 6.47e+01
  bond pdb=" CB  TYR P 441 "
       pdb=" CG  TYR P 441 "
    ideal  model  delta    sigma   weight residual
    1.512  1.445  0.067 2.20e-02 2.07e+03 9.31e+00
  bond pdb=" CG  LEU P 181 "
       pdb=" CD1 LEU P 181 "
    ideal  model  delta    sigma   weight residual
    1.521  1.427  0.094 3.30e-02 9.18e+02 8.04e+00
  bond pdb=" CB  PRO P 137 "
       pdb=" CG  PRO P 137 "
    ideal  model  delta    sigma   weight residual
    1.506  1.400  0.106 3.90e-02 6.57e+02 7.41e+00
  ... (remaining 3143 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.07: 4260
       10.07 -    20.15: 20
       20.15 -    30.22: 1
       30.22 -    40.29: 3
       40.29 -    50.37: 2
  Bond angle restraints: 4286
  Sorted by residual:
  angle pdb=" N   PRO P 399 "
        pdb=" CA  PRO P 399 "
        pdb=" CB  PRO P 399 "
      ideal   model   delta    sigma   weight residual
     102.60   65.95   36.65 1.10e+00 8.26e-01 1.11e+03
  angle pdb=" N   VAL P 118 "
        pdb=" CA  VAL P 118 "
        pdb=" CB  VAL P 118 "
      ideal   model   delta    sigma   weight residual
     110.49   78.16   32.33 1.15e+00 7.56e-01 7.90e+02
  angle pdb=" N   LEU P 398 "
        pdb=" CA  LEU P 398 "
        pdb=" C   LEU P 398 "
      ideal   model   delta    sigma   weight residual
     107.91  149.33  -41.42 2.05e+00 2.38e-01 4.08e+02
  angle pdb=" N   PRO P 399 "
        pdb=" CD  PRO P 399 "
        pdb=" CG  PRO P 399 "
      ideal   model   delta    sigma   weight residual
     103.80   79.83   23.97 1.20e+00 6.94e-01 3.99e+02
  angle pdb=" N   PRO P 399 "
        pdb=" CA  PRO P 399 "
        pdb=" C   PRO P 399 "
      ideal   model   delta    sigma   weight residual
     112.10  162.47  -50.37 2.60e+00 1.48e-01 3.75e+02
  ... (remaining 4281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    10.87: 1509
       10.87 -    21.73: 277
       21.73 -    32.60: 73
       32.60 -    43.46: 16
       43.46 -    54.32: 6
  Dihedral angle restraints: 1881
    sinusoidal: 631
      harmonic: 1250
  Sorted by residual:
  dihedral pdb=" N   VAL P 118 "
           pdb=" C   VAL P 118 "
           pdb=" CA  VAL P 118 "
           pdb=" CB  VAL P 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40   88.32   35.08     0      2.50e+00 1.60e-01 1.97e+02
  dihedral pdb=" CA  LYS P 394 "
           pdb=" C   LYS P 394 "
           pdb=" N   ASN P 395 "
           pdb=" CA  ASN P 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -129.42  -50.58     0      5.00e+00 4.00e-02 1.02e+02
  dihedral pdb=" N   LEU P 398 "
           pdb=" C   LEU P 398 "
           pdb=" CA  LEU P 398 "
           pdb=" CB  LEU P 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  144.26  -21.46     0      2.50e+00 1.60e-01 7.37e+01
  ... (remaining 1878 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.366: 500
       0.366 -    0.732: 1
       0.732 -    1.098: 1
       1.098 -    1.464: 0
       1.464 -    1.829: 2
  Chirality restraints: 504
  Sorted by residual:
  chirality pdb=" CA  PRO P 399 "
            pdb=" N   PRO P 399 "
            pdb=" C   PRO P 399 "
            pdb=" CB  PRO P 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    0.89    1.83 2.00e-01 2.50e+01 8.37e+01
  chirality pdb=" CA  LEU P 398 "
            pdb=" N   LEU P 398 "
            pdb=" C   LEU P 398 "
            pdb=" CB  LEU P 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.99    1.52 2.00e-01 2.50e+01 5.79e+01
  chirality pdb=" CA  ASN P 133 "
            pdb=" N   ASN P 133 "
            pdb=" C   ASN P 133 "
            pdb=" CB  ASN P 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.63    0.88 2.00e-01 2.50e+01 1.94e+01
  ... (remaining 501 not shown)

  Planarity restraints: 564
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU P 398 "    0.143 5.00e-02 4.00e+02   2.09e-01 7.02e+01
        pdb=" N   PRO P 399 "   -0.359 5.00e-02 4.00e+02
        pdb=" CA  PRO P 399 "    0.147 5.00e-02 4.00e+02
        pdb=" CD  PRO P 399 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE P 261 "    0.029 2.00e-02 2.50e+03   2.01e-02 7.10e+00
        pdb=" CG  PHE P 261 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE P 261 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE P 261 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE P 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE P 261 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE P 261 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR P 256 "    0.023 2.00e-02 2.50e+03   1.86e-02 6.89e+00
        pdb=" CG  TYR P 256 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR P 256 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR P 256 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR P 256 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR P 256 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR P 256 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR P 256 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 561 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 45
        2.46 -     3.07: 2532
        3.07 -     3.68: 4232
        3.68 -     4.29: 5645
        4.29 -     4.90: 8788
  Nonbonded interactions: 21242
  Sorted by model distance:
  nonbonded pdb=" O   ASN P 229 "
            pdb=" OD1 ASN P 229 "
     model   vdw
     1.855 3.040
  nonbonded pdb=" CE2 TYR P 117 "
            pdb=" CG2 THR P 152 "
     model   vdw
     1.987 3.760
  nonbonded pdb=" O   LEU P 398 "
            pdb=" CD  PRO P 399 "
     model   vdw
     2.081 2.752
  nonbonded pdb=" O   GLY P 233 "
            pdb=" NH1 ARG P 234 "
     model   vdw
     2.082 3.120
  nonbonded pdb=" OG  SER P  75 "
            pdb=" O   VAL P  78 "
     model   vdw
     2.093 3.040
  ... (remaining 21237 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.140
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.440
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
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      :  0.015   0.200   3148  Z= 0.695
  Angle     :  2.407  50.367   4286  Z= 1.473
  Chirality :  0.139   1.829    504
  Planarity :  0.012   0.209    564
  Dihedral  : 12.691  54.322   1075
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 42.83
  Ramachandran Plot:
    Outliers :  1.16 %
    Allowed  : 16.94 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  6.01 %
    Favored  : 92.58 %
  Cbeta Deviations :  1.49 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 16.67 %
    Twisted General : 1.93 %

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: -6.10 (0.25), residues: 431
  helix: -4.70 (0.36), residues: 55
  sheet: -1.38 (0.90), residues: 28
  loop : -4.65 (0.20), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.005   TRP P 440 
 HIS   0.011   0.005   HIS P  86 
 PHE   0.044   0.006   PHE P  94 
 TYR   0.046   0.005   TYR P 256 
 ARG   0.010   0.002   ARG P 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23777 (   41)
  hydrogen bonds       : angle      12.19687 (  114)
  covalent geometry    : bond        0.01454 ( 3148)
  covalent geometry    : angle       2.40708 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   37 GLN cc_start: 0.8674 (pm20) cc_final: 0.8415 (pm20)
REVERT: P   65 TYR cc_start: 0.8667 (t80) cc_final: 0.8349 (t80)
REVERT: P  109 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6511 (mtt90)
REVERT: P  133 ASN cc_start: 0.7821 (m-40) cc_final: 0.7415 (m-40)
REVERT: P  184 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7947 (mtpt)
REVERT: P  268 THR cc_start: 0.8176 (p) cc_final: 0.7792 (p)
REVERT: P  393 ASP cc_start: 0.7378 (m-30) cc_final: 0.7103 (m-30)
REVERT: P  424 LYS cc_start: 0.8253 (ptmt) cc_final: 0.8004 (ptmt)
  outliers start: 4
  outliers final: 2
  residues processed: 84
  average time/residue: 0.1541
  time to fit residues: 15.7347
Evaluate side-chains
  59 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  207 ILE
Chi-restraints excluded: chain P residue  399 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
P 194 GLN
P 384 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.201455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.187047 restraints weight = 4958.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.190230 restraints weight = 2813.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.192297 restraints weight = 1816.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6732
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3148  Z= 0.181
  Angle     :  0.932  10.519   4286  Z= 0.497
  Chirality :  0.049   0.205    504
  Planarity :  0.006   0.069    564
  Dihedral  :  9.612  34.039    464
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 14.62 %
    Favored  : 84.92 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 12.01 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -5.38 (0.31), residues: 431
  helix: -2.75 (0.61), residues: 54
  sheet: -2.38 (0.75), residues: 50
  loop : -4.32 (0.25), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP P 452 
 HIS   0.003   0.001   HIS P 265 
 PHE   0.019   0.003   PHE P 373 
 TYR   0.024   0.003   TYR P 441 
 ARG   0.004   0.001   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (   41)
  hydrogen bonds       : angle       6.41402 (  114)
  covalent geometry    : bond        0.00364 ( 3148)
  covalent geometry    : angle       0.93228 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: P  154 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6475 (pm20)
REVERT: P  184 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7304 (mtpt)
REVERT: P  219 MET cc_start: 0.6540 (tpp) cc_final: 0.6284 (mmt)
REVERT: P  232 LEU cc_start: 0.6522 (tp) cc_final: 0.6295 (tp)
REVERT: P  384 GLN cc_start: 0.5211 (OUTLIER) cc_final: 0.4258 (pp30)
REVERT: P  431 ASN cc_start: 0.8109 (m-40) cc_final: 0.7790 (m-40)
  outliers start: 16
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1793
  time to fit residues: 17.3104
Evaluate side-chains
  61 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue  116 LYS
Chi-restraints excluded: chain P residue  148 VAL
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  384 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0040
   chunk 32 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0570
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5310

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

Flipped N/Q/H residues before XYZ refinement:
P 384 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.203384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.189074 restraints weight = 4744.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.191935 restraints weight = 2712.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.193908 restraints weight = 1769.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3148  Z= 0.141
  Angle     :  0.813  10.788   4286  Z= 0.429
  Chirality :  0.046   0.158    504
  Planarity :  0.007   0.098    564
  Dihedral  :  8.187  28.912    459
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 12.76 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 17.31 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -5.09 (0.32), residues: 431
  helix: -2.37 (0.63), residues: 61
  sheet: -0.75 (1.06), residues: 28
  loop : -4.24 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP P  57 
 HIS   0.005   0.001   HIS P 415 
 PHE   0.013   0.002   PHE P 373 
 TYR   0.016   0.002   TYR P  83 
 ARG   0.005   0.001   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (   41)
  hydrogen bonds       : angle       5.62026 (  114)
  covalent geometry    : bond        0.00287 ( 3148)
  covalent geometry    : angle       0.81283 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.371 
Fit side-chains
REVERT: P   71 ARG cc_start: 0.7661 (mtm110) cc_final: 0.7205 (ttm110)
REVERT: P  154 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6784 (pm20)
REVERT: P  219 MET cc_start: 0.6488 (tpp) cc_final: 0.6189 (mmt)
REVERT: P  409 MET cc_start: 0.6674 (mtt) cc_final: 0.6450 (mtt)
  outliers start: 14
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1637
  time to fit residues: 14.9694
Evaluate side-chains
  64 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  116 LYS
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  384 GLN
Chi-restraints excluded: chain P residue  454 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 32 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
P  82 GLN
** P 384 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 = 0.4177 r_free = 0.4177 target = 0.201955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.187475 restraints weight = 4973.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.190397 restraints weight = 2845.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.192343 restraints weight = 1849.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3148  Z= 0.141
  Angle     :  0.804  12.872   4286  Z= 0.417
  Chirality :  0.045   0.153    504
  Planarity :  0.006   0.088    564
  Dihedral  :  7.594  27.905    459
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 13.69 %
    Favored  : 85.61 %
  Rotamer:
    Outliers :  8.13 %
    Allowed  : 18.73 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.83 (0.32), residues: 431
  helix: -2.29 (0.61), residues: 61
  sheet: -0.29 (1.16), residues: 28
  loop : -4.06 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP P  57 
 HIS   0.001   0.001   HIS P  91 
 PHE   0.012   0.002   PHE P 373 
 TYR   0.015   0.002   TYR P  83 
 ARG   0.005   0.000   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03183 (   41)
  hydrogen bonds       : angle       5.33762 (  114)
  covalent geometry    : bond        0.00298 ( 3148)
  covalent geometry    : angle       0.80358 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: P   71 ARG cc_start: 0.7410 (mtm110) cc_final: 0.6949 (ttm110)
REVERT: P  154 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6320 (pm20)
REVERT: P  219 MET cc_start: 0.6569 (tpp) cc_final: 0.6236 (mmt)
REVERT: P  395 ASN cc_start: 0.5160 (t0) cc_final: 0.4465 (p0)
REVERT: P  458 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6351 (t)
  outliers start: 23
  outliers final: 13
  residues processed: 82
  average time/residue: 0.1521
  time to fit residues: 14.9921
Evaluate side-chains
  72 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   76 THR
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  181 LEU
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  433 SER
Chi-restraints excluded: chain P residue  439 LEU
Chi-restraints excluded: chain P residue  454 ARG
Chi-restraints excluded: chain P residue  455 ILE
Chi-restraints excluded: chain P residue  458 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0570
   chunk 25 optimal weight:    0.0060
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.6116

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

Flipped N/Q/H residues before XYZ refinement:
P  82 GLN
P 384 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.198535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.183809 restraints weight = 4916.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.186765 restraints weight = 2812.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.188652 restraints weight = 1833.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3148  Z= 0.127
  Angle     :  0.772  13.436   4286  Z= 0.395
  Chirality :  0.044   0.148    504
  Planarity :  0.006   0.082    564
  Dihedral  :  7.108  26.828    459
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 12.76 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 23.32 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.60 (0.33), residues: 431
  helix: -2.12 (0.61), residues: 61
  sheet: -0.29 (1.15), residues: 28
  loop : -3.86 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP P  57 
 HIS   0.001   0.000   HIS P  91 
 PHE   0.011   0.002   PHE P 261 
 TYR   0.017   0.002   TYR P 441 
 ARG   0.003   0.000   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03091 (   41)
  hydrogen bonds       : angle       4.90393 (  114)
  covalent geometry    : bond        0.00267 ( 3148)
  covalent geometry    : angle       0.77204 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: P   71 ARG cc_start: 0.7172 (mtm110) cc_final: 0.6677 (ttm110)
REVERT: P  154 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6388 (pm20)
REVERT: P  265 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.5808 (t-90)
REVERT: P  389 ILE cc_start: 0.7514 (mp) cc_final: 0.7038 (pt)
REVERT: P  395 ASN cc_start: 0.4566 (t0) cc_final: 0.4070 (p0)
REVERT: P  396 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6333 (tm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 72
  average time/residue: 0.1436
  time to fit residues: 12.7874
Evaluate side-chains
  70 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   76 THR
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue   94 PHE
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  161 ASP
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  265 HIS
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  384 GLN
Chi-restraints excluded: chain P residue  439 LEU
Chi-restraints excluded: chain P residue  454 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
P 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.192856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.178427 restraints weight = 5240.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.181135 restraints weight = 3050.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.182803 restraints weight = 2024.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.5000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3148  Z= 0.172
  Angle     :  0.827  13.013   4286  Z= 0.424
  Chirality :  0.046   0.161    504
  Planarity :  0.007   0.111    564
  Dihedral  :  7.364  25.446    459
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 16.24 %
    Favored  : 83.06 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 23.32 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.58 (0.33), residues: 431
  helix: -2.16 (0.61), residues: 59
  sheet: -0.34 (1.13), residues: 28
  loop : -3.83 (0.26), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP P  57 
 HIS   0.003   0.001   HIS P  91 
 PHE   0.019   0.003   PHE P 261 
 TYR   0.019   0.003   TYR P 441 
 ARG   0.003   0.000   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (   41)
  hydrogen bonds       : angle       5.07780 (  114)
  covalent geometry    : bond        0.00385 ( 3148)
  covalent geometry    : angle       0.82683 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.366 
Fit side-chains
REVERT: P   71 ARG cc_start: 0.7347 (mtm110) cc_final: 0.7028 (ttm110)
REVERT: P  154 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6519 (pm20)
REVERT: P  198 LYS cc_start: 0.8393 (ttpp) cc_final: 0.6861 (tppt)
REVERT: P  371 MET cc_start: 0.5638 (mtt) cc_final: 0.5255 (mmm)
REVERT: P  395 ASN cc_start: 0.4741 (t0) cc_final: 0.4183 (p0)
REVERT: P  458 VAL cc_start: 0.6830 (OUTLIER) cc_final: 0.6511 (t)
  outliers start: 20
  outliers final: 14
  residues processed: 73
  average time/residue: 0.1483
  time to fit residues: 13.3963
Evaluate side-chains
  70 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   55 LEU
Chi-restraints excluded: chain P residue   76 THR
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue   94 PHE
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  239 MET
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  439 LEU
Chi-restraints excluded: chain P residue  454 ARG
Chi-restraints excluded: chain P residue  455 ILE
Chi-restraints excluded: chain P residue  458 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.191737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.177278 restraints weight = 5047.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.180059 restraints weight = 2925.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.181899 restraints weight = 1931.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3148  Z= 0.168
  Angle     :  0.823  13.512   4286  Z= 0.422
  Chirality :  0.046   0.159    504
  Planarity :  0.007   0.101    564
  Dihedral  :  7.364  25.364    459
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 16.71 %
    Favored  : 82.60 %
  Rotamer:
    Outliers :  8.13 %
    Allowed  : 23.32 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.48 (0.34), residues: 431
  helix: -1.96 (0.62), residues: 59
  sheet: -0.32 (1.13), residues: 28
  loop : -3.78 (0.27), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP P  57 
 HIS   0.003   0.001   HIS P  91 
 PHE   0.017   0.002   PHE P 261 
 TYR   0.019   0.002   TYR P 441 
 ARG   0.003   0.001   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (   41)
  hydrogen bonds       : angle       5.09568 (  114)
  covalent geometry    : bond        0.00370 ( 3148)
  covalent geometry    : angle       0.82344 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.372 
Fit side-chains
REVERT: P   71 ARG cc_start: 0.7402 (mtm110) cc_final: 0.6983 (ttm110)
REVERT: P   82 GLN cc_start: 0.7753 (mt0) cc_final: 0.6828 (pp30)
REVERT: P  109 ARG cc_start: 0.5894 (mpt180) cc_final: 0.5684 (mtt180)
REVERT: P  154 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6349 (pm20)
REVERT: P  198 LYS cc_start: 0.8463 (ttpp) cc_final: 0.6874 (tppt)
REVERT: P  265 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6461 (t-90)
REVERT: P  424 LYS cc_start: 0.8329 (pttt) cc_final: 0.7801 (ptmt)
REVERT: P  431 ASN cc_start: 0.7503 (m110) cc_final: 0.7068 (t0)
REVERT: P  458 VAL cc_start: 0.6872 (OUTLIER) cc_final: 0.6557 (t)
  outliers start: 23
  outliers final: 16
  residues processed: 77
  average time/residue: 0.1435
  time to fit residues: 13.6349
Evaluate side-chains
  76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   55 LEU
Chi-restraints excluded: chain P residue   76 THR
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue   94 PHE
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  153 ILE
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  239 MET
Chi-restraints excluded: chain P residue  265 HIS
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  433 SER
Chi-restraints excluded: chain P residue  439 LEU
Chi-restraints excluded: chain P residue  454 ARG
Chi-restraints excluded: chain P residue  455 ILE
Chi-restraints excluded: chain P residue  458 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.1382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.198379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.184323 restraints weight = 5142.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.187053 restraints weight = 2980.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.188817 restraints weight = 1966.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.5305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3148  Z= 0.160
  Angle     :  0.848  14.586   4286  Z= 0.423
  Chirality :  0.046   0.155    504
  Planarity :  0.006   0.100    564
  Dihedral  :  7.184  25.593    459
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 16.71 %
    Favored  : 82.60 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 24.03 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.45 (0.34), residues: 431
  helix: -1.84 (0.63), residues: 59
  sheet: -0.30 (1.13), residues: 28
  loop : -3.78 (0.27), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP P  57 
 HIS   0.002   0.001   HIS P  91 
 PHE   0.015   0.002   PHE P 261 
 TYR   0.017   0.002   TYR P 441 
 ARG   0.003   0.000   ARG P 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (   41)
  hydrogen bonds       : angle       5.03124 (  114)
  covalent geometry    : bond        0.00354 ( 3148)
  covalent geometry    : angle       0.84804 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.365 
Fit side-chains
REVERT: P   71 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6819 (ttm110)
REVERT: P   82 GLN cc_start: 0.7702 (mt0) cc_final: 0.6860 (pp30)
REVERT: P  109 ARG cc_start: 0.6009 (mpt180) cc_final: 0.5799 (mtt180)
REVERT: P  154 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6351 (pm20)
REVERT: P  265 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6369 (t-90)
REVERT: P  424 LYS cc_start: 0.8214 (pttt) cc_final: 0.7739 (ptmt)
REVERT: P  458 VAL cc_start: 0.7050 (OUTLIER) cc_final: 0.6732 (t)
  outliers start: 21
  outliers final: 16
  residues processed: 69
  average time/residue: 0.1427
  time to fit residues: 12.1883
Evaluate side-chains
  74 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   48 LEU
Chi-restraints excluded: chain P residue   55 LEU
Chi-restraints excluded: chain P residue   76 THR
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue   94 PHE
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  239 MET
Chi-restraints excluded: chain P residue  265 HIS
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  433 SER
Chi-restraints excluded: chain P residue  439 LEU
Chi-restraints excluded: chain P residue  454 ARG
Chi-restraints excluded: chain P residue  455 ILE
Chi-restraints excluded: chain P residue  458 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 34 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** P 395 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 = 0.4131 r_free = 0.4131 target = 0.196459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.181140 restraints weight = 5096.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.184128 restraints weight = 2895.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.186161 restraints weight = 1880.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3148  Z= 0.175
  Angle     :  0.862  15.063   4286  Z= 0.433
  Chirality :  0.046   0.160    504
  Planarity :  0.007   0.099    564
  Dihedral  :  7.261  24.446    459
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 18.10 %
    Favored  : 81.21 %
  Rotamer:
    Outliers :  8.13 %
    Allowed  : 23.32 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.44 (0.34), residues: 431
  helix: -1.88 (0.63), residues: 61
  sheet: -0.30 (1.14), residues: 28
  loop : -3.77 (0.27), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP P  57 
 HIS   0.003   0.001   HIS P  91 
 PHE   0.018   0.002   PHE P 261 
 TYR   0.019   0.003   TYR P 117 
 ARG   0.002   0.000   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (   41)
  hydrogen bonds       : angle       5.06807 (  114)
  covalent geometry    : bond        0.00391 ( 3148)
  covalent geometry    : angle       0.86181 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.376 
Fit side-chains
REVERT: P   71 ARG cc_start: 0.7390 (mtm110) cc_final: 0.7000 (ttm110)
REVERT: P   82 GLN cc_start: 0.7741 (mt0) cc_final: 0.6831 (pp30)
REVERT: P  109 ARG cc_start: 0.5424 (mpt180) cc_final: 0.5167 (mtt180)
REVERT: P  154 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6211 (pm20)
REVERT: P  265 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6586 (t-90)
REVERT: P  424 LYS cc_start: 0.8348 (pttt) cc_final: 0.7906 (ptmt)
REVERT: P  458 VAL cc_start: 0.7001 (OUTLIER) cc_final: 0.6708 (t)
  outliers start: 23
  outliers final: 17
  residues processed: 69
  average time/residue: 0.1371
  time to fit residues: 11.7972
Evaluate side-chains
  73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   48 LEU
Chi-restraints excluded: chain P residue   55 LEU
Chi-restraints excluded: chain P residue   76 THR
Chi-restraints excluded: chain P residue   86 HIS
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue   94 PHE
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  239 MET
Chi-restraints excluded: chain P residue  265 HIS
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  433 SER
Chi-restraints excluded: chain P residue  439 LEU
Chi-restraints excluded: chain P residue  454 ARG
Chi-restraints excluded: chain P residue  455 ILE
Chi-restraints excluded: chain P residue  458 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0010
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.201109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.186739 restraints weight = 4983.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.189513 restraints weight = 2880.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.191307 restraints weight = 1895.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.5639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3148  Z= 0.141
  Angle     :  0.818  14.944   4286  Z= 0.407
  Chirality :  0.044   0.149    504
  Planarity :  0.006   0.094    564
  Dihedral  :  6.829  23.503    459
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 16.24 %
    Favored  : 83.06 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 23.67 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.33 (0.34), residues: 431
  helix: -1.87 (0.62), residues: 61
  sheet: -0.22 (1.15), residues: 28
  loop : -3.68 (0.27), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP P  57 
 HIS   0.002   0.001   HIS P 415 
 PHE   0.014   0.002   PHE P 261 
 TYR   0.013   0.002   TYR P  83 
 ARG   0.003   0.000   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02980 (   41)
  hydrogen bonds       : angle       4.91335 (  114)
  covalent geometry    : bond        0.00310 ( 3148)
  covalent geometry    : angle       0.81782 ( 4286)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.367 
Fit side-chains
REVERT: P   71 ARG cc_start: 0.7149 (mtm110) cc_final: 0.6773 (ttm110)
REVERT: P   82 GLN cc_start: 0.7749 (mt0) cc_final: 0.7052 (pp30)
REVERT: P  109 ARG cc_start: 0.5426 (mpt180) cc_final: 0.5158 (mtt180)
REVERT: P  154 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6449 (pm20)
REVERT: P  184 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7705 (ttmm)
REVERT: P  239 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6080 (ttp)
REVERT: P  265 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.6434 (t-90)
REVERT: P  431 ASN cc_start: 0.7456 (m110) cc_final: 0.7046 (t0)
REVERT: P  454 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7127 (ptm-80)
REVERT: P  458 VAL cc_start: 0.6989 (OUTLIER) cc_final: 0.6662 (t)
  outliers start: 21
  outliers final: 13
  residues processed: 73
  average time/residue: 0.1353
  time to fit residues: 12.4498
Evaluate side-chains
  73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   76 THR
Chi-restraints excluded: chain P residue   86 HIS
Chi-restraints excluded: chain P residue   92 SER
Chi-restraints excluded: chain P residue   94 PHE
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  103 VAL
Chi-restraints excluded: chain P residue  117 TYR
Chi-restraints excluded: chain P residue  154 GLU
Chi-restraints excluded: chain P residue  165 THR
Chi-restraints excluded: chain P residue  188 ILE
Chi-restraints excluded: chain P residue  239 MET
Chi-restraints excluded: chain P residue  265 HIS
Chi-restraints excluded: chain P residue  373 PHE
Chi-restraints excluded: chain P residue  433 SER
Chi-restraints excluded: chain P residue  439 LEU
Chi-restraints excluded: chain P residue  454 ARG
Chi-restraints excluded: chain P residue  455 ILE
Chi-restraints excluded: chain P residue  458 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 26 optimal weight:    0.2980
   chunk 23 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    0.2980
   chunk 25 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0980
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.205581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.190504 restraints weight = 5058.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.193562 restraints weight = 2900.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.195580 restraints weight = 1887.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.6014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3148  Z= 0.123
  Angle     :  0.792  15.894   4286  Z= 0.385
  Chirality :  0.043   0.141    504
  Planarity :  0.007   0.108    564
  Dihedral  :  6.367  23.147    459
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 14.15 %
    Favored  : 85.15 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 26.50 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 22.22 %
    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: -4.11 (0.34), residues: 431
  helix: -1.65 (0.62), residues: 61
  sheet:  0.47 (1.44), residues: 18
  loop : -3.47 (0.27), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP P  57 
 HIS   0.001   0.001   HIS P 265 
 PHE   0.011   0.002   PHE P 373 
 TYR   0.011   0.002   TYR P 218 
 ARG   0.004   0.000   ARG P 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03030 (   41)
  hydrogen bonds       : angle       4.88197 (  114)
  covalent geometry    : bond        0.00262 ( 3148)
  covalent geometry    : angle       0.79180 ( 4286)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1456.22 seconds
wall clock time: 25 minutes 47.54 seconds (1547.54 seconds total)