Starting phenix.real_space_refine
on Wed Mar  5 22:27:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xoo_33354/03_2025/7xoo_33354.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xoo_33354/03_2025/7xoo_33354.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xoo_33354/03_2025/7xoo_33354.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xoo_33354/03_2025/7xoo_33354.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xoo_33354/03_2025/7xoo_33354.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xoo_33354/03_2025/7xoo_33354.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      20      5.16       5
     C    2397      2.51       5
     N     665      2.21       5
     O     773      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3855
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
  Time building chain proxies: 3.23, per 1000 atoms: 0.84
  Number of scatterers: 3855
  At special positions: 0
  Unit cell: (69.6, 73.95, 85.26, 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      20     16.00
     O     773      8.00
     N     665      7.00
     C    2397      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: 0.92
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  948

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 7 sheets defined
      59.4% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 29
      removed outlier: 4.116A  pdb=" N   VAL B  29 " --> pdb=" O   ASP B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 64 through 86
    Processing helix  chain 'B' and resid 88 through 109
    Processing helix  chain 'B' and resid 112 through 135
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 155 through 170
      removed outlier: 3.598A  pdb=" N   GLY B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 205
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 256 through 268
    Processing helix  chain 'B' and resid 282 through 297
    Processing helix  chain 'B' and resid 338 through 355
      removed outlier: 3.812A  pdb=" N   ILE B 342 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 375
      removed outlier: 4.218A  pdb=" N   GLY B 375 " --> pdb=" O   LYS B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 409
    Processing helix  chain 'B' and resid 416 through 427
    Processing helix  chain 'B' and resid 433 through 459
      Proline residue:  B 450  - end of helix
    Processing helix  chain 'B' and resid 461 through 472
    Processing helix  chain 'B' and resid 488 through 492
    Processing helix  chain 'B' and resid 497 through 516
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 8
    Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40
    Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 179
      removed outlier: 6.423A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ILE B 379 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   THR B 176 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   VAL B 381 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   GLU B 178 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 195
      removed outlier: 6.373A  pdb=" N   GLY B 335 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA B 320 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL B 323 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 195
      removed outlier: 6.373A  pdb=" N   GLY B 335 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA B 320 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   PHE B 219 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ILE B 250 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 247 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   ILE B 249 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 413
    Processing sheet with id=AA7, first strand: chain 'B' and resid 476 through 479

    270 hydrogen bonds defined for protein.
    771 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: 1.29

  Time building geometry restraints manager: 1.10 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: 1339
        1.34 -     1.46: 414
        1.46 -     1.57: 2093
        1.57 -     1.69: 0
        1.69 -     1.80: 37
  Bond restraints: 3883
  Sorted by residual:
  bond pdb=" CB  THR B 522 "
       pdb=" CG2 THR B 522 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.54e+00
  bond pdb=" CB  MET B  16 "
       pdb=" CG  MET B  16 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 6.87e-01
  bond pdb=" CB  MET B 520 "
       pdb=" CG  MET B 520 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.52e-01
  bond pdb=" CA  ALA B 449 "
       pdb=" C   ALA B 449 "
    ideal  model  delta    sigma   weight residual
    1.520  1.530 -0.010 1.23e-02 6.61e+03 6.46e-01
  bond pdb=" C   GLY B  70 "
       pdb=" O   GLY B  70 "
    ideal  model  delta    sigma   weight residual
    1.234  1.243 -0.010 1.21e-02 6.83e+03 6.31e-01
  ... (remaining 3878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 5108
        1.17 -     2.34: 102
        2.34 -     3.52: 29
        3.52 -     4.69: 1
        4.69 -     5.86: 3
  Bond angle restraints: 5243
  Sorted by residual:
  angle pdb=" N   GLY B 306 "
        pdb=" CA  GLY B 306 "
        pdb=" C   GLY B 306 "
      ideal   model   delta    sigma   weight residual
     113.18  119.04   -5.86 2.37e+00 1.78e-01 6.12e+00
  angle pdb=" N   SER B 228 "
        pdb=" CA  SER B 228 "
        pdb=" C   SER B 228 "
      ideal   model   delta    sigma   weight residual
     113.18  110.26    2.92 1.33e+00 5.65e-01 4.83e+00
  angle pdb=" N   ALA B 449 "
        pdb=" CA  ALA B 449 "
        pdb=" C   ALA B 449 "
      ideal   model   delta    sigma   weight residual
     112.75  115.46   -2.71 1.36e+00 5.41e-01 3.98e+00
  angle pdb=" N   GLN B 351 "
        pdb=" CA  GLN B 351 "
        pdb=" CB  GLN B 351 "
      ideal   model   delta    sigma   weight residual
     110.12  112.90   -2.78 1.47e+00 4.63e-01 3.58e+00
  angle pdb=" CB  MET B  69 "
        pdb=" CG  MET B  69 "
        pdb=" SD  MET B  69 "
      ideal   model   delta    sigma   weight residual
     112.70  107.32    5.38 3.00e+00 1.11e-01 3.21e+00
  ... (remaining 5238 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.66: 2218
       15.66 -    31.31: 151
       31.31 -    46.97: 35
       46.97 -    62.62: 3
       62.62 -    78.28: 5
  Dihedral angle restraints: 2412
    sinusoidal: 934
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CA  GLU B 338 "
           pdb=" C   GLU B 338 "
           pdb=" N   GLU B 339 "
           pdb=" CA  GLU B 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.71  -15.29     0      5.00e+00 4.00e-02 9.35e+00
  dihedral pdb=" CG  ARG B 421 "
           pdb=" CD  ARG B 421 "
           pdb=" NE  ARG B 421 "
           pdb=" CZ  ARG B 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -138.97  -41.03     2      1.50e+01 4.44e-03 9.19e+00
  dihedral pdb=" CG  LYS B 132 "
           pdb=" CD  LYS B 132 "
           pdb=" CE  LYS B 132 "
           pdb=" NZ  LYS B 132 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.83   47.83     3      1.50e+01 4.44e-03 8.55e+00
  ... (remaining 2409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 395
       0.028 -    0.057: 154
       0.057 -    0.085: 50
       0.085 -    0.114: 34
       0.114 -    0.142: 5
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  GLU B 102 "
            pdb=" N   GLU B 102 "
            pdb=" C   GLU B 102 "
            pdb=" CB  GLU B 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.04e-01
  chirality pdb=" CA  ILE B 332 "
            pdb=" N   ILE B 332 "
            pdb=" C   ILE B 332 "
            pdb=" CB  ILE B 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  PRO B 462 "
            pdb=" N   PRO B 462 "
            pdb=" C   PRO B 462 "
            pdb=" CB  PRO B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.54e-01
  ... (remaining 635 not shown)

  Planarity restraints: 687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  98 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.56e+00
        pdb=" C   ALA B  98 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ALA B  98 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE B  99 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 233 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.19e+00
        pdb=" C   MET B 233 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   MET B 233 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LEU B 234 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 449 "   -0.015 5.00e-02 4.00e+02   2.26e-02 8.20e-01
        pdb=" N   PRO B 450 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B 450 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B 450 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 684 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1284
        2.85 -     3.36: 4021
        3.36 -     3.87: 6325
        3.87 -     4.39: 6853
        4.39 -     4.90: 12172
  Nonbonded interactions: 30655
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 479 "
            pdb=" OG1 THR B 482 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER B 135 "
            pdb=" OG1 THR B 497 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OE2 GLU B 339 "
            pdb=" NE2 GLN B 343 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" O   PHE B 219 "
            pdb=" N   LEU B 248 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OD1 ASN B 229 "
            pdb=" N   ILE B 230 "
     model   vdw
     2.431 3.120
  ... (remaining 30650 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.020
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.590
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:14.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
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      :  0.003   0.041   3883  Z= 0.214
  Angle     :  0.461   5.862   5243  Z= 0.255
  Chirality :  0.039   0.142    638
  Planarity :  0.002   0.023    687
  Dihedral  : 11.952  78.277   1464
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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:  2.57 (0.36), residues: 522
  helix:  2.86 (0.29), residues: 297
  sheet:  0.25 (0.54), residues: 88
  loop :  0.10 (0.51), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS B 401 
 PHE   0.007   0.001   PHE B 195 
 TYR   0.008   0.001   TYR B 199 
 ARG   0.003   0.000   ARG B 404 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: B  288 MET cc_start: 0.8613 (mtt) cc_final: 0.8396 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 1.6660
  time to fit residues: 46.5269
Evaluate side-chains
  20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.080857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.056146 restraints weight = 9396.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 2.85
r_work: 0.2758 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3883  Z= 0.145
  Angle     :  0.451   6.190   5243  Z= 0.246
  Chirality :  0.040   0.156    638
  Planarity :  0.002   0.020    687
  Dihedral  :  3.520  14.747    552
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  5.20 %
    Favored  : 93.81 %
  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:  2.60 (0.37), residues: 522
  helix:  2.95 (0.29), residues: 304
  sheet:  0.13 (0.55), residues: 88
  loop : -0.14 (0.51), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS B 401 
 PHE   0.014   0.001   PHE B 195 
 TYR   0.005   0.001   TYR B 360 
 ARG   0.003   0.000   ARG B 421 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.472 
Fit side-chains
REVERT: B   69 MET cc_start: 0.7372 (mtp) cc_final: 0.7022 (mtm)
REVERT: B  362 ARG cc_start: 0.9170 (ttp80) cc_final: 0.8961 (ttp-110)
  outliers start: 4
  outliers final: 1
  residues processed: 22
  average time/residue: 1.8425
  time to fit residues: 42.0908
Evaluate side-chains
  21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  522 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:   30.0000
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    6.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.076408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.051375 restraints weight = 9429.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.2795 rms_B_bonded: 2.88
r_work: 0.2632 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   3883  Z= 0.420
  Angle     :  0.544   7.043   5243  Z= 0.292
  Chirality :  0.042   0.147    638
  Planarity :  0.003   0.022    687
  Dihedral  :  3.857  16.541    552
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.92 %
    Favored  : 91.83 %
  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:  2.34 (0.36), residues: 522
  helix:  2.70 (0.28), residues: 301
  sheet:  0.20 (0.59), residues: 80
  loop : -0.16 (0.48), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 401 
 PHE   0.009   0.001   PHE B 195 
 TYR   0.009   0.002   TYR B 199 
 ARG   0.002   0.000   ARG B 404 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: B  518 GLU cc_start: 0.6794 (pt0) cc_final: 0.6135 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 22
  average time/residue: 1.5366
  time to fit residues: 35.2564
Evaluate side-chains
  20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    4.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.077254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.052195 restraints weight = 9534.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 2.86
r_work: 0.2667 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3883  Z= 0.299
  Angle     :  0.486   7.161   5243  Z= 0.260
  Chirality :  0.041   0.144    638
  Planarity :  0.003   0.023    687
  Dihedral  :  3.759  16.607    552
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.41 %
    Favored  : 89.85 %
  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:  2.30 (0.36), residues: 522
  helix:  2.71 (0.28), residues: 302
  sheet:  0.17 (0.58), residues: 88
  loop : -0.32 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B 401 
 PHE   0.012   0.001   PHE B 195 
 TYR   0.007   0.001   TYR B 199 
 ARG   0.002   0.000   ARG B 404 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.440 
Fit side-chains
REVERT: B  307 MET cc_start: 0.8562 (pmt) cc_final: 0.8357 (pmt)
REVERT: B  361 ASP cc_start: 0.9092 (t0) cc_final: 0.8764 (m-30)
REVERT: B  518 GLU cc_start: 0.6749 (pt0) cc_final: 0.6086 (tt0)
  outliers start: 3
  outliers final: 0
  residues processed: 22
  average time/residue: 1.4158
  time to fit residues: 32.4794
Evaluate side-chains
  20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.079318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.055126 restraints weight = 9696.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 2.85
r_work: 0.2738 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3883  Z= 0.144
  Angle     :  0.439   7.941   5243  Z= 0.233
  Chirality :  0.039   0.140    638
  Planarity :  0.002   0.020    687
  Dihedral  :  3.566  14.898    552
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 10.15 %
    Favored  : 89.36 %
  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:  2.47 (0.36), residues: 522
  helix:  2.88 (0.28), residues: 302
  sheet:  0.21 (0.58), residues: 88
  loop : -0.34 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS B 401 
 PHE   0.013   0.001   PHE B 195 
 TYR   0.006   0.001   TYR B 476 
 ARG   0.002   0.000   ARG B 421 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: B   69 MET cc_start: 0.7629 (mtt) cc_final: 0.7427 (mtp)
REVERT: B  361 ASP cc_start: 0.9068 (t0) cc_final: 0.8698 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 22
  average time/residue: 1.4374
  time to fit residues: 33.0432
Evaluate side-chains
  21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0010
   chunk 49 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 24 optimal weight:    0.2980
   chunk 38 optimal weight:    6.9990
   overall best weight:    2.0592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.078851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.054528 restraints weight = 9472.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 2.82
r_work: 0.2727 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3883  Z= 0.177
  Angle     :  0.448   8.757   5243  Z= 0.237
  Chirality :  0.039   0.138    638
  Planarity :  0.002   0.023    687
  Dihedral  :  3.557  15.298    552
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.64 %
    Favored  : 88.61 %
  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:  2.52 (0.36), residues: 522
  helix:  2.91 (0.28), residues: 302
  sheet:  0.28 (0.58), residues: 88
  loop : -0.33 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS B 401 
 PHE   0.013   0.001   PHE B 195 
 TYR   0.006   0.001   TYR B 476 
 ARG   0.001   0.000   ARG B 404 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.449 
Fit side-chains
REVERT: B  361 ASP cc_start: 0.9067 (t0) cc_final: 0.8689 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 24
  average time/residue: 1.2955
  time to fit residues: 32.5306
Evaluate side-chains
  20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.8388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.078768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.054279 restraints weight = 9572.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.84
r_work: 0.2721 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3883  Z= 0.164
  Angle     :  0.451   9.788   5243  Z= 0.237
  Chirality :  0.039   0.138    638
  Planarity :  0.002   0.022    687
  Dihedral  :  3.548  15.157    552
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.89 %
    Favored  : 88.12 %
  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:  2.56 (0.37), residues: 522
  helix:  2.93 (0.29), residues: 302
  sheet:  0.33 (0.59), residues: 88
  loop : -0.32 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS B 401 
 PHE   0.010   0.001   PHE B 195 
 TYR   0.006   0.001   TYR B 476 
 ARG   0.001   0.000   ARG B 421 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.439 
Fit side-chains
REVERT: B  193 MET cc_start: 0.9309 (ptp) cc_final: 0.9063 (ptt)
REVERT: B  361 ASP cc_start: 0.9039 (t0) cc_final: 0.8644 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 24
  average time/residue: 1.2777
  time to fit residues: 32.1644
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  169 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 30 optimal weight:   20.0000
   chunk 49 optimal weight:    0.3980
   chunk 44 optimal weight:    0.0050
   chunk 12 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.2798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.079338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.055007 restraints weight = 9365.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 2.80
r_work: 0.2736 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3883  Z= 0.141
  Angle     :  0.462  11.226   5243  Z= 0.240
  Chirality :  0.038   0.137    638
  Planarity :  0.002   0.022    687
  Dihedral  :  3.485  13.573    552
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.14 %
    Favored  : 88.12 %
  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:  2.60 (0.37), residues: 522
  helix:  2.93 (0.29), residues: 304
  sheet:  0.34 (0.58), residues: 88
  loop : -0.26 (0.49), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS B 401 
 PHE   0.011   0.001   PHE B 195 
 TYR   0.006   0.001   TYR B 476 
 ARG   0.001   0.000   ARG B 421 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.429 
Fit side-chains
REVERT: B  361 ASP cc_start: 0.9029 (t0) cc_final: 0.8630 (m-30)
  outliers start: 3
  outliers final: 3
  residues processed: 23
  average time/residue: 1.1269
  time to fit residues: 27.2882
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  169 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 19 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    4.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.076973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.052154 restraints weight = 9677.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 2.87
r_work: 0.2664 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3883  Z= 0.302
  Angle     :  0.518  12.308   5243  Z= 0.269
  Chirality :  0.040   0.141    638
  Planarity :  0.002   0.023    687
  Dihedral  :  3.637  14.537    552
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.88 %
    Favored  : 87.38 %
  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:  2.48 (0.37), residues: 522
  helix:  2.84 (0.29), residues: 302
  sheet:  0.28 (0.58), residues: 88
  loop : -0.26 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 401 
 PHE   0.009   0.001   PHE B 195 
 TYR   0.006   0.001   TYR B 476 
 ARG   0.002   0.000   ARG B 404 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.474 
Fit side-chains
REVERT: B  193 MET cc_start: 0.9384 (ptp) cc_final: 0.9068 (ptt)
REVERT: B  361 ASP cc_start: 0.9037 (t0) cc_final: 0.8669 (m-30)
  outliers start: 3
  outliers final: 3
  residues processed: 24
  average time/residue: 1.2141
  time to fit residues: 30.5911
Evaluate side-chains
  23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  169 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0060
   chunk 44 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.8004

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.077699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.053117 restraints weight = 9571.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.86
r_work: 0.2689 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3883  Z= 0.221
  Angle     :  0.510  13.266   5243  Z= 0.263
  Chirality :  0.039   0.139    638
  Planarity :  0.002   0.023    687
  Dihedral  :  3.593  14.025    552
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 12.38 %
    Favored  : 87.13 %
  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:  2.43 (0.37), residues: 522
  helix:  2.82 (0.28), residues: 302
  sheet:  0.26 (0.58), residues: 88
  loop : -0.33 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS B 401 
 PHE   0.011   0.001   PHE B 195 
 TYR   0.006   0.001   TYR B 476 
 ARG   0.001   0.000   ARG B 368 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.414 
Fit side-chains
REVERT: B  193 MET cc_start: 0.9395 (ptp) cc_final: 0.9085 (ptt)
REVERT: B  361 ASP cc_start: 0.9008 (t0) cc_final: 0.8609 (m-30)
  outliers start: 2
  outliers final: 2
  residues processed: 22
  average time/residue: 1.2910
  time to fit residues: 29.8242
Evaluate side-chains
  22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 18 optimal weight:   30.0000
   chunk 20 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    3.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.076812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.052032 restraints weight = 9453.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 2.84
r_work: 0.2662 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3883  Z= 0.289
  Angle     :  0.530  13.199   5243  Z= 0.273
  Chirality :  0.040   0.141    638
  Planarity :  0.002   0.024    687
  Dihedral  :  3.659  14.069    552
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 12.38 %
    Favored  : 87.13 %
  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:  2.41 (0.37), residues: 522
  helix:  2.79 (0.29), residues: 302
  sheet:  0.24 (0.59), residues: 88
  loop : -0.29 (0.51), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 401 
 PHE   0.010   0.001   PHE B 195 
 TYR   0.006   0.001   TYR B 476 
 ARG   0.001   0.000   ARG B 404 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2392.93 seconds
wall clock time: 41 minutes 54.67 seconds (2514.67 seconds total)