Starting phenix.real_space_refine
on Tue Mar  3 11:27:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m49_30074/03_2026/6m49_30074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m49_30074/03_2026/6m49_30074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m49_30074/03_2026/6m49_30074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m49_30074/03_2026/6m49_30074.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m49_30074/03_2026/6m49_30074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m49_30074/03_2026/6m49_30074.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.106
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      17      5.16       5
     C    2049      2.51       5
     N     495      2.21       5
     O     537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3098
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1382
          Classifications: {'peptide': 182}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 176}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1687
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 170
          Unresolved non-hydrogen angles: 214
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 81
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'HC3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.78, per 1000 atoms: 0.25
  Number of scatterers: 3098
  At special positions: 0
  Unit cell: (85.873, 78.264, 75.003, 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      17     16.00
     O     537      8.00
     N     495      7.00
     C    2049      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: 0.25
  Conformation dependent library (CDL) restraints added in 122.8 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  778

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 51
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 72 through 96
      Proline residue:  A  89  - end of helix
    Processing helix  chain 'A' and resid 104 through 122
    Processing helix  chain 'A' and resid 130 through 149
    Processing helix  chain 'A' and resid 153 through 173
      removed outlier: 3.607A  pdb=" N   LEU A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 189
    Processing helix  chain 'A' and resid 190 through 214
      removed outlier: 4.262A  pdb=" N   CYS A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLU A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 4.025A  pdb=" N   TYR B  25 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 47
      Proline residue:  B  43  - end of helix
      removed outlier: 3.765A  pdb=" N   LYS B  46 " --> pdb=" O   TYR B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 305
    Processing helix  chain 'B' and resid 313 through 338
      removed outlier: 4.050A  pdb=" N   LEU B 317 " --> pdb=" O   TRP B 313 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU B 336 " --> pdb=" O   GLY B 332 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY B 338 " --> pdb=" O   CYS B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 357
      Proline residue:  B 350  - end of helix
    Processing helix  chain 'B' and resid 358 through 370
      removed outlier: 3.663A  pdb=" N   LEU B 362 " --> pdb=" O   LEU B 358 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   LEU B 364 " --> pdb=" O   ASN B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 387
    Processing helix  chain 'B' and resid 388 through 408
    Processing helix  chain 'B' and resid 411 through 449
      removed outlier: 4.347A  pdb=" N   THR B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 556

    269 hydrogen bonds defined for protein.
    804 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: 0.47

  Time building geometry restraints manager: 0.32 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 944
        1.34 -     1.46: 744
        1.46 -     1.58: 1450
        1.58 -     1.69: 0
        1.69 -     1.81: 25
  Bond restraints: 3163
  Sorted by residual:
  bond pdb=" N   VAL B 309 "
       pdb=" CA  VAL B 309 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.30e-02 5.92e+03 9.09e+00
  bond pdb=" N   ARG A  53 "
       pdb=" CA  ARG A  53 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.16e-02 7.43e+03 7.81e+00
  bond pdb=" N   GLU B 376 "
       pdb=" CA  GLU B 376 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.035 1.27e-02 6.20e+03 7.79e+00
  bond pdb=" N   GLN A  50 "
       pdb=" CA  GLN A  50 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.30e-02 5.92e+03 7.32e+00
  bond pdb=" N   VAL B 377 "
       pdb=" CA  VAL B 377 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 6.97e+00
  ... (remaining 3158 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 4067
        1.56 -     3.13: 201
        3.13 -     4.69: 46
        4.69 -     6.25: 9
        6.25 -     7.82: 2
  Bond angle restraints: 4325
  Sorted by residual:
  angle pdb=" CA  VAL B 309 "
        pdb=" C   VAL B 309 "
        pdb=" O   VAL B 309 "
      ideal   model   delta    sigma   weight residual
     121.58  117.64    3.94 1.00e+00 1.00e+00 1.55e+01
  angle pdb=" CA  ASP B 374 "
        pdb=" C   ASP B 374 "
        pdb=" O   ASP B 374 "
      ideal   model   delta    sigma   weight residual
     120.66  116.41    4.25 1.15e+00 7.56e-01 1.36e+01
  angle pdb=" C   ASP B 307 "
        pdb=" N   MET B 308 "
        pdb=" CA  MET B 308 "
      ideal   model   delta    sigma   weight residual
     122.21  127.93   -5.72 1.62e+00 3.81e-01 1.25e+01
  angle pdb=" C   VAL B 309 "
        pdb=" N   LYS B 310 "
        pdb=" CA  LYS B 310 "
      ideal   model   delta    sigma   weight residual
     122.40  127.49   -5.09 1.45e+00 4.76e-01 1.23e+01
  angle pdb=" N   VAL B 373 "
        pdb=" CA  VAL B 373 "
        pdb=" C   VAL B 373 "
      ideal   model   delta    sigma   weight residual
     111.77  108.19    3.58 1.04e+00 9.25e-01 1.19e+01
  ... (remaining 4320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.05: 1623
       14.05 -    28.10: 161
       28.10 -    42.15: 71
       42.15 -    56.19: 12
       56.19 -    70.24: 3
  Dihedral angle restraints: 1870
    sinusoidal: 667
      harmonic: 1203
  Sorted by residual:
  dihedral pdb=" CA  LEU B 285 "
           pdb=" C   LEU B 285 "
           pdb=" N   ILE B 286 "
           pdb=" CA  ILE B 286 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.83  -19.17     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  TRP A  72 "
           pdb=" C   TRP A  72 "
           pdb=" N   VAL A  73 "
           pdb=" CA  VAL A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.41  -18.59     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  MET A 212 "
           pdb=" C   MET A 212 "
           pdb=" N   TYR A 213 "
           pdb=" CA  TYR A 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.38   16.62     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 1867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 401
       0.049 -    0.098: 114
       0.098 -    0.147: 19
       0.147 -    0.195: 4
       0.195 -    0.244: 2
  Chirality restraints: 540
  Sorted by residual:
  chirality pdb=" C10 HC3 A 501 "
            pdb=" C1  HC3 A 501 "
            pdb=" C5  HC3 A 501 "
            pdb=" C9  HC3 A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.61   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  VAL B 377 "
            pdb=" N   VAL B 377 "
            pdb=" C   VAL B 377 "
            pdb=" CB  VAL B 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  GLU A 104 "
            pdb=" N   GLU A 104 "
            pdb=" C   GLU A 104 "
            pdb=" CB  GLU A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.13e-01
  ... (remaining 537 not shown)

  Planarity restraints: 522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 373 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.67e+00
        pdb=" C   VAL B 373 "    0.045 2.00e-02 2.50e+03
        pdb=" O   VAL B 373 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP B 374 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 433 "    0.013 2.00e-02 2.50e+03   2.54e-02 6.44e+00
        pdb=" C   MET B 433 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   MET B 433 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B 434 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  11 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.59e+00
        pdb=" C   ILE B  11 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ILE B  11 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER B  12 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 519 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 61
        2.64 -     3.21: 3474
        3.21 -     3.77: 4776
        3.77 -     4.34: 5906
        4.34 -     4.90: 9329
  Nonbonded interactions: 23546
  Sorted by model distance:
  nonbonded pdb=" O   GLN A  52 "
            pdb=" NE2 GLN A  52 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" O   ARG A  53 "
            pdb=" OD1 ASN A  54 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   GLY B 406 "
            pdb=" OG1 THR B 409 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   PHE A 163 "
            pdb=" OG1 THR A 166 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   PRO B 287 "
            pdb=" OG1 THR B 291 "
     model   vdw
     2.299 3.040
  ... (remaining 23541 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:             0.480
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     4.720
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
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      :  0.008   0.056   3163  Z= 0.398
  Angle     :  0.851   7.815   4325  Z= 0.500
  Chirality :  0.048   0.244    540
  Planarity :  0.005   0.034    522
  Dihedral  : 14.047  70.242   1092
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.11 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.89 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.00 (0.35), residues: 408
  helix: -2.04 (0.24), residues: 330
  sheet:  None (None), residues: 0
  loop : -4.52 (0.55), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 208 
 TYR   0.015   0.002   TYR B 298 
 PHE   0.023   0.002   PHE B 429 
 TRP   0.018   0.002   TRP B 313 
 HIS   0.008   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00828 ( 3163)
  covalent geometry    : angle       0.85080 ( 4325)
  hydrogen bonds       : bond        0.12557 (  269)
  hydrogen bonds       : angle       6.50229 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8511 (ttm) cc_final: 0.8305 (tmm)
REVERT: A  102 LYS cc_start: 0.7823 (mttt) cc_final: 0.7198 (mtmt)
REVERT: A  119 ASN cc_start: 0.8384 (t0) cc_final: 0.8107 (t0)
REVERT: A  172 LEU cc_start: 0.8320 (pp) cc_final: 0.8078 (pp)
REVERT: A  214 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7619 (tm-30)
REVERT: B  344 ASN cc_start: 0.7140 (p0) cc_final: 0.6653 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0644
  time to fit residues: 9.8054
Evaluate side-chains
  89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.175890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.144048 restraints weight = 6310.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.149081 restraints weight = 3561.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.150803 restraints weight = 2133.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.151319 restraints weight = 1855.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.152507 restraints weight = 1796.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   3163  Z= 0.154
  Angle     :  0.717   7.660   4325  Z= 0.352
  Chirality :  0.039   0.108    540
  Planarity :  0.004   0.027    522
  Dihedral  :  5.343  55.178    501
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.34 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.40), residues: 408
  helix:  0.72 (0.27), residues: 336
  sheet:  None (None), residues: 0
  loop : -3.69 (0.63), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 380 
 TYR   0.010   0.001   TYR B  16 
 PHE   0.014   0.001   PHE A 148 
 TRP   0.017   0.001   TRP A 191 
 HIS   0.006   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3163)
  covalent geometry    : angle       0.71669 ( 4325)
  hydrogen bonds       : bond        0.04284 (  269)
  hydrogen bonds       : angle       3.96487 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 PHE cc_start: 0.8450 (t80) cc_final: 0.8093 (t80)
REVERT: A  102 LYS cc_start: 0.8381 (mttt) cc_final: 0.7866 (ttmt)
REVERT: B  298 TYR cc_start: 0.8368 (t80) cc_final: 0.6739 (t80)
REVERT: B  329 MET cc_start: 0.8377 (ttm) cc_final: 0.8144 (ttm)
  outliers start: 11
  outliers final: 6
  residues processed: 110
  average time/residue: 0.0510
  time to fit residues: 7.0983
Evaluate side-chains
  92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain B residue   36 CYS
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0040
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0970
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 ASN
A 170 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.156894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.125742 restraints weight = 6240.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.129234 restraints weight = 3346.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.131121 restraints weight = 2272.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.131239 restraints weight = 1743.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.131814 restraints weight = 1682.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.4816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3163  Z= 0.133
  Angle     :  0.702   9.630   4325  Z= 0.335
  Chirality :  0.039   0.121    540
  Planarity :  0.004   0.030    522
  Dihedral  :  5.512  53.034    501
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 26.89 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.42), residues: 408
  helix:  2.03 (0.28), residues: 337
  sheet:  None (None), residues: 0
  loop : -3.38 (0.62), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  31 
 TYR   0.013   0.001   TYR B 351 
 PHE   0.011   0.001   PHE A 148 
 TRP   0.011   0.001   TRP A 191 
 HIS   0.007   0.003   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3163)
  covalent geometry    : angle       0.70206 ( 4325)
  hydrogen bonds       : bond        0.03890 (  269)
  hydrogen bonds       : angle       3.57861 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   41 PHE cc_start: 0.8446 (t80) cc_final: 0.8240 (t80)
REVERT: A   47 ASN cc_start: 0.8343 (t0) cc_final: 0.8058 (t0)
REVERT: A  102 LYS cc_start: 0.7886 (mttt) cc_final: 0.7216 (ttpt)
REVERT: A  104 GLU cc_start: 0.6078 (mp0) cc_final: 0.5839 (mp0)
REVERT: A  119 ASN cc_start: 0.8613 (t160) cc_final: 0.8412 (t0)
REVERT: B  296 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: B  329 MET cc_start: 0.8254 (ttm) cc_final: 0.7946 (ttm)
REVERT: B  383 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7986 (mm-40)
REVERT: B  396 MET cc_start: 0.7160 (mmm) cc_final: 0.6846 (mtt)
  outliers start: 8
  outliers final: 3
  residues processed: 110
  average time/residue: 0.0540
  time to fit residues: 7.4364
Evaluate side-chains
  93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  296 PHE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  443 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0010
   chunk 13 optimal weight:    0.2980
   chunk 39 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.155369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.123278 restraints weight = 6160.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.126102 restraints weight = 3392.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.127868 restraints weight = 2480.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.128046 restraints weight = 1861.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.128799 restraints weight = 1791.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3163  Z= 0.135
  Angle     :  0.695  10.339   4325  Z= 0.337
  Chirality :  0.039   0.121    540
  Planarity :  0.004   0.034    522
  Dihedral  :  5.307  51.958    501
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 25.57 %
    Favored  : 68.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.43), residues: 408
  helix:  2.18 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -3.30 (0.58), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 380 
 TYR   0.013   0.001   TYR B 351 
 PHE   0.009   0.001   PHE A 148 
 TRP   0.010   0.001   TRP A 191 
 HIS   0.006   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3163)
  covalent geometry    : angle       0.69480 ( 4325)
  hydrogen bonds       : bond        0.03936 (  269)
  hydrogen bonds       : angle       3.52695 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8450 (ptp) cc_final: 0.7931 (ppp)
REVERT: A   47 ASN cc_start: 0.8448 (t0) cc_final: 0.8195 (t0)
REVERT: A   50 GLN cc_start: 0.7051 (pt0) cc_final: 0.6847 (pt0)
REVERT: A   72 TRP cc_start: 0.6582 (m-10) cc_final: 0.6360 (m-10)
REVERT: A  102 LYS cc_start: 0.7819 (mttt) cc_final: 0.7542 (ttpt)
REVERT: A  119 ASN cc_start: 0.8702 (t160) cc_final: 0.8474 (t0)
REVERT: B  296 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7604 (t80)
REVERT: B  329 MET cc_start: 0.8332 (ttm) cc_final: 0.8025 (ttm)
REVERT: B  383 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8128 (mm-40)
REVERT: B  396 MET cc_start: 0.7333 (mmm) cc_final: 0.6851 (mtt)
  outliers start: 17
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0472
  time to fit residues: 6.6314
Evaluate side-chains
  103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  296 PHE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  366 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.153876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.121474 restraints weight = 6199.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.124133 restraints weight = 3543.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.126026 restraints weight = 2541.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.126418 restraints weight = 1847.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.127024 restraints weight = 1759.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.5609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3163  Z= 0.132
  Angle     :  0.690  10.492   4325  Z= 0.332
  Chirality :  0.039   0.129    540
  Planarity :  0.004   0.057    522
  Dihedral  :  5.262  54.353    501
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 29.18 %
    Favored  : 65.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.42), residues: 408
  helix:  2.24 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.21 (0.59), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 380 
 TYR   0.010   0.001   TYR B  16 
 PHE   0.009   0.001   PHE A 148 
 TRP   0.019   0.001   TRP B 313 
 HIS   0.005   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3163)
  covalent geometry    : angle       0.69024 ( 4325)
  hydrogen bonds       : bond        0.03793 (  269)
  hydrogen bonds       : angle       3.46461 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8395 (ptp) cc_final: 0.7812 (ppp)
REVERT: A   47 ASN cc_start: 0.8436 (t0) cc_final: 0.8202 (t0)
REVERT: A  102 LYS cc_start: 0.7872 (mttt) cc_final: 0.7476 (ttpt)
REVERT: B  296 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7701 (t80)
REVERT: B  298 TYR cc_start: 0.8500 (t80) cc_final: 0.7426 (t80)
REVERT: B  383 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8199 (mm-40)
REVERT: B  396 MET cc_start: 0.7417 (mmm) cc_final: 0.6882 (mtt)
  outliers start: 17
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0449
  time to fit residues: 6.1578
Evaluate side-chains
  105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  296 PHE
Chi-restraints excluded: chain B residue  313 TRP
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  400 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 3 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.151797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.119201 restraints weight = 6196.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.121867 restraints weight = 3562.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.123556 restraints weight = 2563.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.123579 restraints weight = 1933.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.124236 restraints weight = 1893.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.5911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3163  Z= 0.137
  Angle     :  0.695  11.569   4325  Z= 0.338
  Chirality :  0.040   0.129    540
  Planarity :  0.004   0.053    522
  Dihedral  :  5.284  57.291    501
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 27.54 %
    Favored  : 65.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.42), residues: 408
  helix:  2.26 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.08 (0.61), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  31 
 TYR   0.020   0.001   TYR B 351 
 PHE   0.010   0.001   PHE A 148 
 TRP   0.014   0.001   TRP B 313 
 HIS   0.006   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3163)
  covalent geometry    : angle       0.69516 ( 4325)
  hydrogen bonds       : bond        0.03963 (  269)
  hydrogen bonds       : angle       3.48465 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8437 (ptp) cc_final: 0.7813 (ppp)
REVERT: A   47 ASN cc_start: 0.8413 (t0) cc_final: 0.8107 (t0)
REVERT: A   92 ASP cc_start: 0.9053 (m-30) cc_final: 0.8809 (m-30)
REVERT: A  102 LYS cc_start: 0.8050 (mttt) cc_final: 0.7385 (ttmt)
REVERT: B  286 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8167 (tt)
REVERT: B  296 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7777 (t80)
REVERT: B  298 TYR cc_start: 0.8604 (t80) cc_final: 0.7561 (t80)
REVERT: B  329 MET cc_start: 0.8324 (ttm) cc_final: 0.8112 (ttm)
REVERT: B  396 MET cc_start: 0.7444 (mmm) cc_final: 0.6912 (mtt)
  outliers start: 20
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0465
  time to fit residues: 6.6601
Evaluate side-chains
  106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  296 PHE
Chi-restraints excluded: chain B residue  313 TRP
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  400 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 383 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.152899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.119428 restraints weight = 6223.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.120600 restraints weight = 3447.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.122896 restraints weight = 2678.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.122908 restraints weight = 1960.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.123494 restraints weight = 2004.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.6183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3163  Z= 0.132
  Angle     :  0.723  12.088   4325  Z= 0.344
  Chirality :  0.040   0.142    540
  Planarity :  0.004   0.054    522
  Dihedral  :  5.247  56.530    501
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 31.15 %
    Favored  : 63.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.42), residues: 408
  helix:  2.27 (0.27), residues: 339
  sheet:  None (None), residues: 0
  loop : -3.00 (0.61), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 189 
 TYR   0.017   0.001   TYR B 351 
 PHE   0.011   0.001   PHE A 148 
 TRP   0.013   0.001   TRP B 313 
 HIS   0.005   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3163)
  covalent geometry    : angle       0.72319 ( 4325)
  hydrogen bonds       : bond        0.03735 (  269)
  hydrogen bonds       : angle       3.45700 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8432 (ptp) cc_final: 0.7791 (ppp)
REVERT: A   47 ASN cc_start: 0.8389 (t0) cc_final: 0.8114 (t0)
REVERT: A  102 LYS cc_start: 0.7839 (mttt) cc_final: 0.7445 (ttpt)
REVERT: B  286 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7979 (tt)
REVERT: B  298 TYR cc_start: 0.8531 (t80) cc_final: 0.7362 (t80)
REVERT: B  396 MET cc_start: 0.7434 (mmm) cc_final: 0.6926 (mtt)
  outliers start: 16
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0460
  time to fit residues: 6.2802
Evaluate side-chains
  104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 GLN
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:   20.0000
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 GLN
** B 383 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 = 0.4200 r_free = 0.4200 target = 0.147208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.113632 restraints weight = 6459.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.115746 restraints weight = 3611.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.117332 restraints weight = 2596.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.117488 restraints weight = 2041.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.118133 restraints weight = 2110.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.6382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3163  Z= 0.175
  Angle     :  0.775  10.879   4325  Z= 0.380
  Chirality :  0.047   0.428    540
  Planarity :  0.005   0.053    522
  Dihedral  :  5.475  58.361    501
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 31.48 %
    Favored  : 62.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.42), residues: 408
  helix:  2.17 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -2.58 (0.67), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 380 
 TYR   0.013   0.002   TYR B  16 
 PHE   0.020   0.001   PHE A  41 
 TRP   0.012   0.001   TRP A 191 
 HIS   0.005   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 3163)
  covalent geometry    : angle       0.77479 ( 4325)
  hydrogen bonds       : bond        0.04463 (  269)
  hydrogen bonds       : angle       3.69247 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8419 (ptp) cc_final: 0.7768 (ppp)
REVERT: A   47 ASN cc_start: 0.8479 (t0) cc_final: 0.8230 (t0)
REVERT: A   75 PRO cc_start: 0.7940 (Cg_exo) cc_final: 0.7699 (Cg_endo)
REVERT: A  102 LYS cc_start: 0.8100 (mttt) cc_final: 0.7278 (ttmt)
REVERT: B   15 PHE cc_start: 0.8911 (m-80) cc_final: 0.8704 (m-10)
REVERT: B  286 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8238 (tt)
REVERT: B  296 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7858 (t80)
REVERT: B  298 TYR cc_start: 0.8704 (t80) cc_final: 0.7846 (t80)
REVERT: B  329 MET cc_start: 0.8357 (ttm) cc_final: 0.8154 (ttm)
REVERT: B  344 ASN cc_start: 0.6892 (p0) cc_final: 0.6381 (p0)
REVERT: B  383 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8258 (mp10)
REVERT: B  396 MET cc_start: 0.7496 (mmm) cc_final: 0.6992 (mtt)
  outliers start: 18
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0427
  time to fit residues: 5.9819
Evaluate side-chains
  115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  296 PHE
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 GLN
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.0970
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 383 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.150579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.115902 restraints weight = 6301.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.119007 restraints weight = 3529.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.120559 restraints weight = 2374.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120483 restraints weight = 1917.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120876 restraints weight = 2018.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.6588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3163  Z= 0.143
  Angle     :  0.784  11.794   4325  Z= 0.372
  Chirality :  0.045   0.404    540
  Planarity :  0.004   0.054    522
  Dihedral  :  5.320  59.298    501
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 35.41 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.41), residues: 408
  helix:  2.16 (0.27), residues: 340
  sheet:  None (None), residues: 0
  loop : -2.64 (0.66), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  31 
 TYR   0.011   0.001   TYR B  16 
 PHE   0.019   0.001   PHE A  41 
 TRP   0.012   0.001   TRP A 105 
 HIS   0.006   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3163)
  covalent geometry    : angle       0.78421 ( 4325)
  hydrogen bonds       : bond        0.03969 (  269)
  hydrogen bonds       : angle       3.61707 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8427 (ptp) cc_final: 0.7782 (ppp)
REVERT: A   47 ASN cc_start: 0.8354 (t0) cc_final: 0.8049 (t0)
REVERT: A   75 PRO cc_start: 0.7762 (Cg_exo) cc_final: 0.7525 (Cg_endo)
REVERT: A  102 LYS cc_start: 0.7982 (mttt) cc_final: 0.7212 (ttmt)
REVERT: B  286 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8095 (tt)
REVERT: B  298 TYR cc_start: 0.8614 (t80) cc_final: 0.7663 (t80)
REVERT: B  383 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8429 (mt0)
REVERT: B  396 MET cc_start: 0.7484 (mmm) cc_final: 0.6929 (mtt)
  outliers start: 14
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0428
  time to fit residues: 5.7396
Evaluate side-chains
  108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 GLN
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0980
   chunk 34 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0370
   chunk 12 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5660

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 383 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.152189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.118324 restraints weight = 6127.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.120564 restraints weight = 3294.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.122345 restraints weight = 2460.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.122443 restraints weight = 1887.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.123057 restraints weight = 1968.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.6740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3163  Z= 0.141
  Angle     :  0.834  15.398   4325  Z= 0.385
  Chirality :  0.045   0.400    540
  Planarity :  0.005   0.055    522
  Dihedral  :  5.240  59.087    501
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 36.07 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.41), residues: 408
  helix:  2.23 (0.27), residues: 339
  sheet:  None (None), residues: 0
  loop : -2.59 (0.65), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 189 
 TYR   0.018   0.001   TYR B 351 
 PHE   0.019   0.001   PHE A  41 
 TRP   0.014   0.001   TRP A 105 
 HIS   0.005   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3163)
  covalent geometry    : angle       0.83356 ( 4325)
  hydrogen bonds       : bond        0.03891 (  269)
  hydrogen bonds       : angle       3.57499 (  804)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8403 (ptp) cc_final: 0.7771 (ppp)
REVERT: A   47 ASN cc_start: 0.8369 (t0) cc_final: 0.8080 (t0)
REVERT: A   75 PRO cc_start: 0.7716 (Cg_exo) cc_final: 0.7477 (Cg_endo)
REVERT: A  100 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8203 (mtmm)
REVERT: A  102 LYS cc_start: 0.7819 (mttt) cc_final: 0.7340 (ttpt)
REVERT: B  286 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8005 (tt)
REVERT: B  298 TYR cc_start: 0.8511 (t80) cc_final: 0.7537 (t80)
REVERT: B  396 MET cc_start: 0.7527 (mmm) cc_final: 0.7103 (mtt)
  outliers start: 12
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0435
  time to fit residues: 5.9671
Evaluate side-chains
  108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  383 GLN
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 36 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 383 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.152056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.118101 restraints weight = 6216.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.120438 restraints weight = 3394.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.122405 restraints weight = 2466.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.122245 restraints weight = 1885.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.122942 restraints weight = 1979.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.6841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3163  Z= 0.143
  Angle     :  0.809  14.968   4325  Z= 0.382
  Chirality :  0.045   0.403    540
  Planarity :  0.005   0.055    522
  Dihedral  :  5.062  56.692    501
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 36.07 %
    Favored  : 59.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.41), residues: 408
  helix:  2.18 (0.27), residues: 339
  sheet:  None (None), residues: 0
  loop : -2.47 (0.65), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 380 
 TYR   0.013   0.001   TYR B  16 
 PHE   0.019   0.001   PHE A  41 
 TRP   0.013   0.001   TRP A 105 
 HIS   0.005   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3163)
  covalent geometry    : angle       0.80945 ( 4325)
  hydrogen bonds       : bond        0.03876 (  269)
  hydrogen bonds       : angle       3.59043 (  804)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 710.15 seconds
wall clock time: 12 minutes 56.92 seconds (776.92 seconds total)