Starting phenix.real_space_refine
on Mon Feb 10 23:10:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m49_30074/02_2025/6m49_30074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m49_30074/02_2025/6m49_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_30074/02_2025/6m49_30074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m49_30074/02_2025/6m49_30074.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m49_30074/02_2025/6m49_30074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m49_30074/02_2025/6m49_30074.cif"
  }
  resolution = 3.7
  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=   0.007 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'PHE:plan': 2, 'TYR:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7}
          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: 2.31, per 1000 atoms: 0.75
  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: 0.79
  Conformation dependent library (CDL) restraints added in 374.3 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: 0.23
  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: 0.70

  Time building geometry restraints manager: 0.87 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:             0.320
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.080
-------------------------------------------------------------------------------
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= 0.537
  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 (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: -4.00 (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
 TRP   0.018   0.002   TRP B 313 
 HIS   0.008   0.002   HIS A 120 
 PHE   0.023   0.002   PHE B 429 
 TYR   0.015   0.002   TYR B 298 
 ARG   0.004   0.001   ARG A 208 

*********************** 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  : 0.473 
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  129 ASN cc_start: 0.8272 (t0) cc_final: 0.7950 (p0)
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: 0.1591
  time to fit residues: 24.0969
Evaluate side-chains
  90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.198144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.165570 restraints weight = 5252.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.171159 restraints weight = 2751.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.172690 restraints weight = 1741.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   3163  Z= 0.222
  Angle     :  0.712   7.619   4325  Z= 0.349
  Chirality :  0.038   0.109    540
  Planarity :  0.004   0.029    522
  Dihedral  :  5.238  53.634    501
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.69 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.40), residues: 408
  helix:  0.76 (0.27), residues: 336
  sheet:  None (None), residues: 0
  loop : -3.68 (0.63), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 191 
 HIS   0.006   0.002   HIS A 120 
 PHE   0.014   0.001   PHE A 148 
 TYR   0.011   0.001   TYR B  16 
 ARG   0.002   0.000   ARG A 110 

*********************** 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
  113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 PHE cc_start: 0.8433 (t80) cc_final: 0.8077 (t80)
REVERT: A  102 LYS cc_start: 0.8352 (mttt) cc_final: 0.7862 (ttmt)
REVERT: A  132 GLN cc_start: 0.8341 (mm110) cc_final: 0.7711 (mm-40)
REVERT: B  329 MET cc_start: 0.8238 (ttm) cc_final: 0.7999 (ttm)
  outliers start: 9
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1252
  time to fit residues: 16.5720
Evaluate side-chains
  86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain B residue   36 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.153977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.122621 restraints weight = 6107.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.126311 restraints weight = 3259.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.127792 restraints weight = 2202.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3163  Z= 0.200
  Angle     :  0.701   9.459   4325  Z= 0.337
  Chirality :  0.039   0.112    540
  Planarity :  0.004   0.029    522
  Dihedral  :  5.593  53.919    501
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 23.61 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.42), residues: 408
  helix:  1.97 (0.28), residues: 337
  sheet:  None (None), residues: 0
  loop : -3.28 (0.61), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 191 
 HIS   0.007   0.003   HIS A 120 
 PHE   0.013   0.001   PHE A 127 
 TYR   0.013   0.001   TYR B 351 
 ARG   0.003   0.000   ARG B 380 

*********************** 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
  115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 PHE cc_start: 0.8486 (t80) cc_final: 0.8215 (t80)
REVERT: A   47 ASN cc_start: 0.8309 (t0) cc_final: 0.8047 (t0)
REVERT: A  102 LYS cc_start: 0.7905 (mttt) cc_final: 0.7293 (ttmt)
REVERT: A  104 GLU cc_start: 0.6233 (mp0) cc_final: 0.6008 (mp0)
REVERT: B  296 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7719 (t80)
REVERT: B  298 TYR cc_start: 0.8325 (t80) cc_final: 0.6343 (t80)
REVERT: B  329 MET cc_start: 0.8383 (ttm) cc_final: 0.8026 (ttm)
REVERT: B  383 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8042 (mm-40)
REVERT: B  396 MET cc_start: 0.7170 (mmm) cc_final: 0.6857 (mtt)
  outliers start: 12
  outliers final: 6
  residues processed: 106
  average time/residue: 0.1253
  time to fit residues: 16.4525
Evaluate side-chains
  94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  296 PHE
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  381 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 30 optimal weight:    0.3980
   chunk 15 optimal weight:    0.4980
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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
A 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.151887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.119468 restraints weight = 6230.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.123554 restraints weight = 3390.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.124846 restraints weight = 2230.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   3163  Z= 0.222
  Angle     :  0.718  13.170   4325  Z= 0.347
  Chirality :  0.039   0.117    540
  Planarity :  0.004   0.033    522
  Dihedral  :  5.403  55.060    501
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 25.25 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.43), residues: 408
  helix:  2.13 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.22 (0.60), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 191 
 HIS   0.007   0.002   HIS A 120 
 PHE   0.009   0.001   PHE A 148 
 TYR   0.013   0.001   TYR B 351 
 ARG   0.002   0.000   ARG A  31 

*********************** 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: 18
    poor density    : 100
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8441 (ptp) cc_final: 0.7954 (ppp)
REVERT: A   50 GLN cc_start: 0.7196 (pt0) cc_final: 0.6931 (pt0)
REVERT: A  100 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8399 (mtmm)
REVERT: A  102 LYS cc_start: 0.7829 (mttt) cc_final: 0.7387 (ttpt)
REVERT: A  133 LEU cc_start: 0.7759 (tp) cc_final: 0.7283 (tp)
REVERT: B  286 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8159 (tt)
REVERT: B  296 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7664 (t80)
REVERT: B  298 TYR cc_start: 0.8489 (t80) cc_final: 0.6398 (t80)
REVERT: B  329 MET cc_start: 0.8365 (ttm) cc_final: 0.7977 (ttm)
REVERT: B  383 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8146 (mm-40)
REVERT: B  396 MET cc_start: 0.7345 (mmm) cc_final: 0.6934 (mtt)
REVERT: B  443 ASP cc_start: 0.9018 (t70) cc_final: 0.8706 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 110
  average time/residue: 0.1260
  time to fit residues: 17.3007
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  : 0.322 
-------------------------------------------------------------------------------
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  119 ASN
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain B residue   36 CYS
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  362 LEU
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 15 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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
A 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.150041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.110007 restraints weight = 6204.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.114492 restraints weight = 3313.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.117487 restraints weight = 2299.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.5664

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= 0.204
  Angle     :  0.701  12.800   4325  Z= 0.337
  Chirality :  0.039   0.122    540
  Planarity :  0.004   0.035    522
  Dihedral  :  5.439  56.760    501
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 28.52 %
    Favored  : 64.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.42), residues: 408
  helix:  2.15 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.16 (0.61), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 191 
 HIS   0.004   0.001   HIS A 120 
 PHE   0.010   0.001   PHE A 148 
 TYR   0.011   0.001   TYR B 351 
 ARG   0.002   0.000   ARG A 208 

*********************** 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
  121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8380 (ptp) cc_final: 0.7841 (ppp)
REVERT: A   47 ASN cc_start: 0.8723 (t0) cc_final: 0.8490 (t0)
REVERT: A  100 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8368 (mtmm)
REVERT: A  102 LYS cc_start: 0.7918 (mttt) cc_final: 0.7002 (ttmt)
REVERT: A  104 GLU cc_start: 0.6650 (mp0) cc_final: 0.6263 (mp0)
REVERT: B  296 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7714 (t80)
REVERT: B  298 TYR cc_start: 0.8582 (t80) cc_final: 0.6291 (t80)
REVERT: B  329 MET cc_start: 0.8385 (ttm) cc_final: 0.8015 (ttm)
REVERT: B  383 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8203 (mm-40)
REVERT: B  396 MET cc_start: 0.7415 (mmm) cc_final: 0.6894 (mtt)
  outliers start: 21
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1169
  time to fit residues: 16.3702
Evaluate side-chains
  107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
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  129 ASN
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain B residue   37 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  327 LEU
Chi-restraints excluded: chain B residue  352 LEU
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  400 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0770
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.153216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.119205 restraints weight = 6295.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.121192 restraints weight = 3382.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.123380 restraints weight = 2526.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.5962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   3163  Z= 0.183
  Angle     :  0.701  13.137   4325  Z= 0.333
  Chirality :  0.039   0.137    540
  Planarity :  0.004   0.058    522
  Dihedral  :  5.266  56.452    501
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 31.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.42), residues: 408
  helix:  2.25 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -3.16 (0.60), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 191 
 HIS   0.007   0.002   HIS A 120 
 PHE   0.020   0.001   PHE A 127 
 TYR   0.012   0.001   TYR B 351 
 ARG   0.001   0.000   ARG A 189 

*********************** 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
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8453 (ptp) cc_final: 0.7870 (ppp)
REVERT: A   47 ASN cc_start: 0.8612 (t0) cc_final: 0.8334 (t0)
REVERT: A   92 ASP cc_start: 0.9079 (m-30) cc_final: 0.8842 (m-30)
REVERT: A  100 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8345 (mtmm)
REVERT: A  102 LYS cc_start: 0.7889 (mttt) cc_final: 0.7521 (ttpt)
REVERT: A  155 PHE cc_start: 0.8401 (t80) cc_final: 0.8133 (t80)
REVERT: B  296 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7690 (t80)
REVERT: B  298 TYR cc_start: 0.8465 (t80) cc_final: 0.7480 (t80)
REVERT: B  329 MET cc_start: 0.8398 (ttm) cc_final: 0.8117 (ttm)
REVERT: B  383 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8282 (mm-40)
REVERT: B  396 MET cc_start: 0.7436 (mmm) cc_final: 0.6972 (mtt)
REVERT: B  400 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7425 (tt)
  outliers start: 14
  outliers final: 8
  residues processed: 111
  average time/residue: 0.1256
  time to fit residues: 17.4531
Evaluate side-chains
  106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue  129 ASN
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  296 PHE
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  352 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 0 optimal weight:   20.0000
   chunk 14 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.151064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.118455 restraints weight = 6240.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.120788 restraints weight = 3600.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.122662 restraints weight = 2615.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.6115

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= 0.195
  Angle     :  0.714  13.899   4325  Z= 0.340
  Chirality :  0.040   0.152    540
  Planarity :  0.004   0.055    522
  Dihedral  :  5.361  59.460    501
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 32.79 %
    Favored  : 61.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.42), residues: 408
  helix:  2.21 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -3.19 (0.59), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 191 
 HIS   0.006   0.002   HIS A 120 
 PHE   0.016   0.001   PHE A 115 
 TYR   0.017   0.001   TYR B 351 
 ARG   0.001   0.000   ARG A  31 

*********************** 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
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8442 (ptp) cc_final: 0.7806 (ppp)
REVERT: A   47 ASN cc_start: 0.8647 (t0) cc_final: 0.8423 (t0)
REVERT: A   92 ASP cc_start: 0.9100 (m-30) cc_final: 0.8880 (m-30)
REVERT: A  100 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8427 (mtmm)
REVERT: A  102 LYS cc_start: 0.7885 (mttt) cc_final: 0.7448 (ttpt)
REVERT: B  286 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8100 (tt)
REVERT: B  296 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7685 (t80)
REVERT: B  298 TYR cc_start: 0.8528 (t80) cc_final: 0.6315 (t80)
REVERT: B  383 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8257 (mm-40)
REVERT: B  396 MET cc_start: 0.7445 (mmm) cc_final: 0.6907 (mtt)
  outliers start: 18
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1248
  time to fit residues: 16.9973
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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  129 ASN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  144 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  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
Chi-restraints excluded: chain B residue  403 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.151299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.118054 restraints weight = 6316.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.119078 restraints weight = 3604.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.121385 restraints weight = 2818.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.6286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   3163  Z= 0.197
  Angle     :  0.753  12.976   4325  Z= 0.355
  Chirality :  0.042   0.220    540
  Planarity :  0.004   0.054    522
  Dihedral  :  5.318  58.875    501
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 32.46 %
    Favored  : 62.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.42), residues: 408
  helix:  2.23 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -3.19 (0.59), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 105 
 HIS   0.006   0.002   HIS A 120 
 PHE   0.019   0.001   PHE A  41 
 TYR   0.023   0.001   TYR B 351 
 ARG   0.001   0.000   ARG A  31 

*********************** 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
  117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8411 (ptp) cc_final: 0.7759 (ppp)
REVERT: A   47 ASN cc_start: 0.8611 (t0) cc_final: 0.8335 (t0)
REVERT: A   75 PRO cc_start: 0.7930 (Cg_exo) cc_final: 0.7700 (Cg_endo)
REVERT: A   92 ASP cc_start: 0.9106 (m-30) cc_final: 0.8901 (m-30)
REVERT: A  102 LYS cc_start: 0.7863 (mttt) cc_final: 0.7426 (ttpt)
REVERT: A  190 SER cc_start: 0.8651 (t) cc_final: 0.8434 (p)
REVERT: B  286 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8087 (tt)
REVERT: B  296 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: B  298 TYR cc_start: 0.8490 (t80) cc_final: 0.6346 (t80)
REVERT: B  383 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8295 (mm-40)
REVERT: B  396 MET cc_start: 0.7394 (mmm) cc_final: 0.6863 (mtt)
  outliers start: 16
  outliers final: 14
  residues processed: 111
  average time/residue: 0.1114
  time to fit residues: 15.5028
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
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  137 LEU
Chi-restraints excluded: chain A residue  144 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  295 LEU
Chi-restraints excluded: chain B residue  296 PHE
Chi-restraints excluded: chain B residue  327 LEU
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  400 LEU
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 19 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0870
   overall best weight:    1.2164

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.149787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.117659 restraints weight = 6353.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.120719 restraints weight = 3580.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.122506 restraints weight = 2449.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.6468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   3163  Z= 0.221
  Angle     :  0.753  12.089   4325  Z= 0.361
  Chirality :  0.042   0.200    540
  Planarity :  0.004   0.054    522
  Dihedral  :  5.463  59.843    501
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 33.77 %
    Favored  : 60.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.41), residues: 408
  helix:  2.11 (0.27), residues: 339
  sheet:  None (None), residues: 0
  loop : -3.08 (0.61), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 105 
 HIS   0.006   0.002   HIS A 120 
 PHE   0.019   0.001   PHE A  41 
 TYR   0.010   0.001   TYR B  16 
 ARG   0.002   0.000   ARG A 150 

*********************** 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
  117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8422 (ptp) cc_final: 0.7772 (ppp)
REVERT: A   47 ASN cc_start: 0.8672 (t0) cc_final: 0.8454 (t0)
REVERT: A   75 PRO cc_start: 0.7911 (Cg_exo) cc_final: 0.7653 (Cg_endo)
REVERT: A  102 LYS cc_start: 0.8034 (mttt) cc_final: 0.7247 (ttmt)
REVERT: A  133 LEU cc_start: 0.7838 (tp) cc_final: 0.7464 (tp)
REVERT: A  190 SER cc_start: 0.8517 (t) cc_final: 0.8268 (p)
REVERT: B  286 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8167 (tt)
REVERT: B  296 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7705 (t80)
REVERT: B  298 TYR cc_start: 0.8632 (t80) cc_final: 0.6565 (t80)
REVERT: B  383 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8212 (mm-40)
REVERT: B  396 MET cc_start: 0.7639 (mmm) cc_final: 0.7027 (mtt)
REVERT: B  429 PHE cc_start: 0.7931 (t80) cc_final: 0.7677 (t80)
  outliers start: 17
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1184
  time to fit residues: 16.2932
Evaluate side-chains
  114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  137 LEU
Chi-restraints excluded: chain A residue  144 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  295 LEU
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  400 LEU
Chi-restraints excluded: chain B residue  405 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 3 optimal weight:    0.0570
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 39 optimal weight:    8.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
** A 119 ASN ** 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 = 0.4268 r_free = 0.4268 target = 0.152558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.119560 restraints weight = 6141.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.120429 restraints weight = 3556.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.122888 restraints weight = 2791.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.6620

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= 0.198
  Angle     :  0.773  11.510   4325  Z= 0.367
  Chirality :  0.042   0.198    540
  Planarity :  0.005   0.055    522
  Dihedral  :  5.182  55.993    501
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 35.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.42), residues: 408
  helix:  2.19 (0.27), residues: 340
  sheet:  None (None), residues: 0
  loop : -2.97 (0.62), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 105 
 HIS   0.006   0.002   HIS A 120 
 PHE   0.020   0.001   PHE A  41 
 TYR   0.012   0.001   TYR B  16 
 ARG   0.002   0.000   ARG A  93 

********************** 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
  115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8398 (ptp) cc_final: 0.7771 (ppp)
REVERT: A   47 ASN cc_start: 0.8578 (t0) cc_final: 0.8358 (t0)
REVERT: A   75 PRO cc_start: 0.7699 (Cg_exo) cc_final: 0.7459 (Cg_endo)
REVERT: A  102 LYS cc_start: 0.7837 (mttt) cc_final: 0.7418 (ttpt)
REVERT: A  133 LEU cc_start: 0.7728 (tp) cc_final: 0.7402 (tp)
REVERT: A  190 SER cc_start: 0.8676 (t) cc_final: 0.8437 (p)
REVERT: B  286 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8073 (tt)
REVERT: B  298 TYR cc_start: 0.8399 (t80) cc_final: 0.7524 (t80)
REVERT: B  365 THR cc_start: 0.8573 (p) cc_final: 0.8241 (t)
REVERT: B  374 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6740 (t0)
REVERT: B  396 MET cc_start: 0.7540 (mmm) cc_final: 0.6924 (mtt)
REVERT: B  429 PHE cc_start: 0.7874 (t80) cc_final: 0.7534 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1278
  time to fit residues: 17.0892
Evaluate side-chains
  114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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 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  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  374 ASP
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  400 LEU
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 20 optimal weight:    0.2980
   chunk 14 optimal weight:    6.9990
   chunk 28 optimal weight:    0.4980
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   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 119 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 = 0.4253 r_free = 0.4253 target = 0.151535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.118184 restraints weight = 6241.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.119564 restraints weight = 3594.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.121688 restraints weight = 2739.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.6766

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= 0.206
  Angle     :  0.764  11.270   4325  Z= 0.369
  Chirality :  0.042   0.209    540
  Planarity :  0.005   0.055    522
  Dihedral  :  5.003  51.951    501
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 35.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.42), residues: 408
  helix:  2.09 (0.28), residues: 342
  sheet:  None (None), residues: 0
  loop : -2.96 (0.63), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 105 
 HIS   0.014   0.004   HIS A  99 
 PHE   0.019   0.001   PHE A  41 
 TYR   0.012   0.001   TYR B  16 
 ARG   0.001   0.000   ARG A 189 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1306.11 seconds
wall clock time: 24 minutes 4.16 seconds (1444.16 seconds total)