Starting phenix.real_space_refine
on Fri Aug 22 16:00:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gv5_51624/08_2025/9gv5_51624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gv5_51624/08_2025/9gv5_51624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gv5_51624/08_2025/9gv5_51624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gv5_51624/08_2025/9gv5_51624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gv5_51624/08_2025/9gv5_51624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gv5_51624/08_2025/9gv5_51624.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    1806      2.51       5
     N     421      2.21       5
     O     446      1.98       5
     H    2766      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5465
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 5465
          Classifications: {'peptide': 355}
          Link IDs: {'PTRANS': 15, 'TRANS': 339}
          Chain breaks: 2
  Time building chain proxies: 1.15, per 1000 atoms: 0.21
  Number of scatterers: 5465
  At special positions: 0
  Unit cell: (67.32, 65.824, 65.824, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      26     16.00
     O     446      8.00
     N     421      7.00
     C    1806      6.00
     H    2766      1.00
    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: 0.43
  Conformation dependent library (CDL) restraints added in 119.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  632

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      89.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 100 through 128
      removed outlier: 3.658A  pdb=" N   PHE A 115 " --> pdb=" O   ASN A 111 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   GLY A 122 " --> pdb=" O   HIS A 118 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 157
      removed outlier: 4.180A  pdb=" N   ALA A 144 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   PHE A 155 " --> pdb=" O   MET A 151 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   CYS A 157 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 187
      removed outlier: 3.895A  pdb=" N   ILE A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   CYS A 170 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 9.452A  pdb=" N   ARG A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   HIS A 186 " --> pdb=" O   PHE A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 214
      removed outlier: 3.879A  pdb=" N   LEU A 204 " --> pdb=" O   THR A 200 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLN A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 218
      removed outlier: 3.745A  pdb=" N   VAL A 218 " --> pdb=" O   PRO A 215 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 215 through 218'
    Processing helix  chain 'A' and resid 219 through 224
      removed outlier: 3.967A  pdb=" N   TYR A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 254
      Proline residue:  A 247  - end of helix
    Processing helix  chain 'A' and resid 258 through 266
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 4.298A  pdb=" N   MET A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 336
      removed outlier: 3.867A  pdb=" N   GLY A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   PHE A 336 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 350
      removed outlier: 3.939A  pdb=" N   GLU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
      removed outlier: 4.914A  pdb=" N   THR A 366 " --> pdb=" O   CYS A 362 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 385
      removed outlier: 4.056A  pdb=" N   LYS A 385 " --> pdb=" O   PRO A 382 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 382 through 385'
    Processing helix  chain 'A' and resid 386 through 403
      removed outlier: 3.837A  pdb=" N   GLN A 390 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 408
      removed outlier: 3.630A  pdb=" N   ARG A 408 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 429
      removed outlier: 3.941A  pdb=" N   VAL A 415 " --> pdb=" O   GLY A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 440
    Processing helix  chain 'A' and resid 443 through 471
      removed outlier: 4.309A  pdb=" N   LEU A 457 " --> pdb=" O   GLY A 453 " (cutoff:3.500A)
      Proline residue:  A 458  - end of helix
      Proline residue:  A 463  - end of helix
      removed outlier: 4.502A  pdb=" N   ASN A 471 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 480
    Processing helix  chain 'A' and resid 481 through 483
      No H-bonds generated for 'chain 'A' and resid 481 through 483'
    Processing helix  chain 'A' and resid 484 through 491

    197 hydrogen bonds defined for protein.
    591 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: 0.79

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2756
        1.03 -     1.23: 10
        1.23 -     1.42: 1173
        1.42 -     1.61: 1558
        1.61 -     1.81: 42
  Bond restraints: 5539
  Sorted by residual:
  bond pdb=" N   GLY A 112 "
       pdb=" CA  GLY A 112 "
    ideal  model  delta    sigma   weight residual
    1.454  1.443  0.012 1.23e-02 6.61e+03 8.76e-01
  bond pdb=" CA  VAL A 485 "
       pdb=" CB  VAL A 485 "
    ideal  model  delta    sigma   weight residual
    1.534  1.539 -0.005 6.80e-03 2.16e+04 4.96e-01
  bond pdb=" CA  GLY A 112 "
       pdb=" C   GLY A 112 "
    ideal  model  delta    sigma   weight residual
    1.517  1.510  0.008 1.08e-02 8.57e+03 4.86e-01
  bond pdb=" CA  LYS A 258 "
       pdb=" C   LYS A 258 "
    ideal  model  delta    sigma   weight residual
    1.523  1.532 -0.008 1.34e-02 5.57e+03 3.96e-01
  bond pdb=" CG  GLN A 390 "
       pdb=" CD  GLN A 390 "
    ideal  model  delta    sigma   weight residual
    1.516  1.503  0.013 2.50e-02 1.60e+03 2.71e-01
  ... (remaining 5534 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 9194
        1.01 -     2.03: 764
        2.03 -     3.04: 42
        3.04 -     4.06: 11
        4.06 -     5.07: 3
  Bond angle restraints: 10014
  Sorted by residual:
  angle pdb=" N   ILE A 363 "
        pdb=" CA  ILE A 363 "
        pdb=" C   ILE A 363 "
      ideal   model   delta    sigma   weight residual
     112.96  108.75    4.21 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" C   ALA A 491 "
        pdb=" N   VAL A 492 "
        pdb=" CA  VAL A 492 "
      ideal   model   delta    sigma   weight residual
     122.97  120.90    2.07 9.80e-01 1.04e+00 4.48e+00
  angle pdb=" N   CYS A 472 "
        pdb=" CA  CYS A 472 "
        pdb=" C   CYS A 472 "
      ideal   model   delta    sigma   weight residual
     112.72  110.30    2.42 1.28e+00 6.10e-01 3.58e+00
  angle pdb=" N   SER A 188 "
        pdb=" CA  SER A 188 "
        pdb=" C   SER A 188 "
      ideal   model   delta    sigma   weight residual
     113.23  111.00    2.23 1.22e+00 6.72e-01 3.35e+00
  angle pdb=" CA  ILE A 363 "
        pdb=" C   ILE A 363 "
        pdb=" N   GLY A 364 "
      ideal   model   delta    sigma   weight residual
     118.65  116.83    1.82 1.07e+00 8.73e-01 2.90e+00
  ... (remaining 10009 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 2384
       17.13 -    34.25: 145
       34.25 -    51.38: 48
       51.38 -    68.51: 46
       68.51 -    85.63: 1
  Dihedral angle restraints: 2624
    sinusoidal: 1367
      harmonic: 1257
  Sorted by residual:
  dihedral pdb=" CA  TYR A 335 "
           pdb=" C   TYR A 335 "
           pdb=" N   PHE A 336 "
           pdb=" CA  PHE A 336 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.15  -17.85     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  THR A 187 "
           pdb=" C   THR A 187 "
           pdb=" N   SER A 188 "
           pdb=" CA  SER A 188 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.21  -16.79     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  PHE A 155 "
           pdb=" C   PHE A 155 "
           pdb=" N   PHE A 156 "
           pdb=" CA  PHE A 156 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.59  -15.41     0      5.00e+00 4.00e-02 9.50e+00
  ... (remaining 2621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 280
       0.026 -    0.052: 83
       0.052 -    0.078: 42
       0.078 -    0.104: 24
       0.104 -    0.130: 4
  Chirality restraints: 433
  Sorted by residual:
  chirality pdb=" CA  ILE A 353 "
            pdb=" N   ILE A 353 "
            pdb=" C   ILE A 353 "
            pdb=" CB  ILE A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE A 381 "
            pdb=" N   ILE A 381 "
            pdb=" C   ILE A 381 "
            pdb=" CB  ILE A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CA  PRO A 338 "
            pdb=" N   PRO A 338 "
            pdb=" C   PRO A 338 "
            pdb=" CB  PRO A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.83e-01
  ... (remaining 430 not shown)

  Planarity restraints: 796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 463 "   -0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO A 464 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 464 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 464 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 485 "    0.021 5.00e-02 4.00e+02   3.12e-02 1.56e+00
        pdb=" N   PRO A 486 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 486 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 486 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 199 "    0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" C   PHE A 199 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   PHE A 199 "    0.008 2.00e-02 2.50e+03
        pdb=" N   THR A 200 "    0.007 2.00e-02 2.50e+03
  ... (remaining 793 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 842
        2.28 -     2.86: 12553
        2.86 -     3.44: 14256
        3.44 -     4.02: 17868
        4.02 -     4.60: 27977
  Nonbonded interactions: 73496
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 355 "
            pdb=" H   LEU A 359 "
     model   vdw
     1.696 2.450
  nonbonded pdb="HH11 ARG A 171 "
            pdb=" O   LEU A 278 "
     model   vdw
     1.700 2.450
  nonbonded pdb=" O   MET A 274 "
            pdb=" HG  SER A 277 "
     model   vdw
     1.708 2.450
  nonbonded pdb=" O   LYS A 386 "
            pdb=" H   LEU A 389 "
     model   vdw
     1.748 2.450
  nonbonded pdb=" O   LYS A 385 "
            pdb=" H   TYR A 388 "
     model   vdw
     1.821 2.450
  ... (remaining 73491 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.840
  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:             0.030
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.920
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
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      :  0.002   0.022   2773  Z= 0.122
  Angle     :  0.522   5.075   3760  Z= 0.306
  Chirality :  0.037   0.130    433
  Planarity :  0.004   0.039    459
  Dihedral  : 11.201  85.633    945
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  4.21 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.48), residues: 349
  helix:  1.29 (0.33), residues: 262
  sheet:  None (None), residues: 0
  loop : -2.07 (0.71), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.012   0.001   TYR A 125 
 PHE   0.012   0.001   PHE A 182 
 TRP   0.004   0.001   TRP A 109 
 HIS   0.002   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 2773)
  covalent geometry    : angle       0.52167 ( 3760)
  hydrogen bonds       : bond        0.09153 (  197)
  hydrogen bonds       : angle       5.55211 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7575 (tppt) cc_final: 0.7366 (mmmt)
REVERT: A  274 MET cc_start: 0.8157 (ttp) cc_final: 0.7363 (tpp)
REVERT: A  403 MET cc_start: 0.5926 (tpp) cc_final: 0.5621 (tpp)
REVERT: A  408 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6149 (tpt170)
REVERT: A  437 GLU cc_start: 0.7526 (tp30) cc_final: 0.7322 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0729
  time to fit residues: 7.7408
Evaluate side-chains
  71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4311 r_free = 0.4311 target = 0.158134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.134374 restraints weight = 21924.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.140825 restraints weight = 10724.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.145089 restraints weight = 6240.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.147955 restraints weight = 4060.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.149731 restraints weight = 2884.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6298
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2773  Z= 0.149
  Angle     :  0.548   4.949   3760  Z= 0.306
  Chirality :  0.038   0.132    433
  Planarity :  0.005   0.037    459
  Dihedral  :  4.777  18.742    373
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 10.18 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.46), residues: 349
  helix:  1.12 (0.32), residues: 259
  sheet:  None (None), residues: 0
  loop : -2.30 (0.66), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 171 
 TYR   0.011   0.001   TYR A 125 
 PHE   0.012   0.001   PHE A 426 
 TRP   0.005   0.001   TRP A 109 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2773)
  covalent geometry    : angle       0.54774 ( 3760)
  hydrogen bonds       : bond        0.04329 (  197)
  hydrogen bonds       : angle       5.45705 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8074 (mmp) cc_final: 0.7806 (mmp)
REVERT: A  274 MET cc_start: 0.8824 (ttp) cc_final: 0.7876 (tpp)
REVERT: A  339 TYR cc_start: 0.7279 (t80) cc_final: 0.7055 (t80)
REVERT: A  403 MET cc_start: 0.5587 (tpp) cc_final: 0.5311 (tpp)
REVERT: A  408 ARG cc_start: 0.6846 (mtp85) cc_final: 0.5986 (tpt170)
  outliers start: 1
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0706
  time to fit residues: 6.4658
Evaluate side-chains
  69 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 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 = 0.4301 r_free = 0.4301 target = 0.157344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.133916 restraints weight = 21483.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.140301 restraints weight = 10614.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.144558 restraints weight = 6185.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.147319 restraints weight = 4045.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.149177 restraints weight = 2896.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2773  Z= 0.138
  Angle     :  0.540   4.874   3760  Z= 0.298
  Chirality :  0.038   0.137    433
  Planarity :  0.004   0.037    459
  Dihedral  :  4.666  17.253    373
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.53 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.46), residues: 349
  helix:  1.09 (0.32), residues: 263
  sheet:  None (None), residues: 0
  loop : -2.11 (0.69), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 371 
 TYR   0.010   0.001   TYR A 125 
 PHE   0.010   0.001   PHE A 182 
 TRP   0.005   0.001   TRP A 109 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2773)
  covalent geometry    : angle       0.54031 ( 3760)
  hydrogen bonds       : bond        0.04089 (  197)
  hydrogen bonds       : angle       5.40198 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8092 (mmp) cc_final: 0.7781 (mmp)
REVERT: A  274 MET cc_start: 0.8873 (ttp) cc_final: 0.7942 (tpp)
REVERT: A  403 MET cc_start: 0.5665 (tpp) cc_final: 0.5382 (tpp)
REVERT: A  408 ARG cc_start: 0.6881 (mtp85) cc_final: 0.6098 (tpt170)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.0649
  time to fit residues: 5.9109
Evaluate side-chains
  70 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 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 = 0.4321 r_free = 0.4321 target = 0.158265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.134905 restraints weight = 21902.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.141330 restraints weight = 10856.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.145715 restraints weight = 6328.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.148513 restraints weight = 4086.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.150339 restraints weight = 2887.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6246
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2773  Z= 0.125
  Angle     :  0.524   4.901   3760  Z= 0.286
  Chirality :  0.037   0.137    433
  Planarity :  0.005   0.038    459
  Dihedral  :  4.561  17.177    373
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 12.28 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.46), residues: 349
  helix:  1.21 (0.32), residues: 263
  sheet:  None (None), residues: 0
  loop : -1.99 (0.71), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 371 
 TYR   0.010   0.001   TYR A 125 
 PHE   0.020   0.001   PHE A 182 
 TRP   0.004   0.001   TRP A 109 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 2773)
  covalent geometry    : angle       0.52399 ( 3760)
  hydrogen bonds       : bond        0.03866 (  197)
  hydrogen bonds       : angle       5.31034 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8065 (mmp) cc_final: 0.7767 (mmp)
REVERT: A  274 MET cc_start: 0.8890 (ttp) cc_final: 0.7876 (tpp)
REVERT: A  403 MET cc_start: 0.5694 (tpp) cc_final: 0.5426 (tpp)
REVERT: A  408 ARG cc_start: 0.6871 (mtp85) cc_final: 0.6070 (tpt170)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.0863
  time to fit residues: 7.5558
Evaluate side-chains
  71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 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 = 0.4287 r_free = 0.4287 target = 0.155688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.132132 restraints weight = 22264.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.138754 restraints weight = 10865.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.142926 restraints weight = 6269.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.145652 restraints weight = 4110.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.147444 restraints weight = 2935.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6358
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2773  Z= 0.186
  Angle     :  0.576   4.784   3760  Z= 0.325
  Chirality :  0.038   0.137    433
  Planarity :  0.005   0.036    459
  Dihedral  :  4.750  15.546    373
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 14.39 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.45), residues: 349
  helix:  0.71 (0.32), residues: 260
  sheet:  None (None), residues: 0
  loop : -2.24 (0.66), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 226 
 TYR   0.013   0.002   TYR A 201 
 PHE   0.014   0.001   PHE A 224 
 TRP   0.006   0.001   TRP A 109 
 HIS   0.004   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2773)
  covalent geometry    : angle       0.57566 ( 3760)
  hydrogen bonds       : bond        0.04126 (  197)
  hydrogen bonds       : angle       5.56801 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8171 (mmp) cc_final: 0.7881 (mmp)
REVERT: A  274 MET cc_start: 0.8858 (ttp) cc_final: 0.7973 (tpp)
REVERT: A  403 MET cc_start: 0.5686 (tpp) cc_final: 0.5418 (tpp)
REVERT: A  408 ARG cc_start: 0.6890 (mtp85) cc_final: 0.6050 (tpt170)
  outliers start: 2
  outliers final: 2
  residues processed: 68
  average time/residue: 0.0687
  time to fit residues: 6.1120
Evaluate side-chains
  70 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0470
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 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 = 0.4309 r_free = 0.4309 target = 0.157264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.134006 restraints weight = 21881.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.140628 restraints weight = 10737.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.144799 restraints weight = 6153.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.147553 restraints weight = 3995.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.149201 restraints weight = 2825.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6286
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2773  Z= 0.126
  Angle     :  0.538   4.838   3760  Z= 0.294
  Chirality :  0.037   0.138    433
  Planarity :  0.005   0.037    459
  Dihedral  :  4.620  17.762    373
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 14.39 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.46), residues: 349
  helix:  0.98 (0.32), residues: 265
  sheet:  None (None), residues: 0
  loop : -1.93 (0.72), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 371 
 TYR   0.008   0.001   TYR A 125 
 PHE   0.010   0.001   PHE A 182 
 TRP   0.003   0.001   TRP A 109 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 2773)
  covalent geometry    : angle       0.53760 ( 3760)
  hydrogen bonds       : bond        0.03771 (  197)
  hydrogen bonds       : angle       5.33821 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8105 (mmp) cc_final: 0.7787 (mmp)
REVERT: A  274 MET cc_start: 0.8844 (ttp) cc_final: 0.7942 (tpp)
REVERT: A  403 MET cc_start: 0.5649 (tpp) cc_final: 0.5420 (tpp)
REVERT: A  408 ARG cc_start: 0.6840 (mtp85) cc_final: 0.6031 (tpt170)
  outliers start: 2
  outliers final: 2
  residues processed: 73
  average time/residue: 0.0700
  time to fit residues: 6.5710
Evaluate side-chains
  73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   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 118 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 = 0.4308 r_free = 0.4308 target = 0.157109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.133784 restraints weight = 21940.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.140394 restraints weight = 10746.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.144607 restraints weight = 6181.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.147293 restraints weight = 4003.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.149075 restraints weight = 2835.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6278
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2773  Z= 0.133
  Angle     :  0.539   4.771   3760  Z= 0.298
  Chirality :  0.037   0.137    433
  Planarity :  0.005   0.042    459
  Dihedral  :  4.552  15.661    373
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 16.84 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.47), residues: 349
  helix:  1.02 (0.32), residues: 266
  sheet:  None (None), residues: 0
  loop : -1.82 (0.75), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.010   0.001   TYR A 201 
 PHE   0.009   0.001   PHE A 199 
 TRP   0.006   0.001   TRP A 109 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 2773)
  covalent geometry    : angle       0.53928 ( 3760)
  hydrogen bonds       : bond        0.03803 (  197)
  hydrogen bonds       : angle       5.33466 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8114 (mmp) cc_final: 0.7800 (mmp)
REVERT: A  274 MET cc_start: 0.8828 (ttp) cc_final: 0.7916 (tpp)
REVERT: A  403 MET cc_start: 0.5656 (tpp) cc_final: 0.5424 (tpp)
REVERT: A  408 ARG cc_start: 0.6831 (mtp85) cc_final: 0.6029 (tpt170)
  outliers start: 1
  outliers final: 1
  residues processed: 70
  average time/residue: 0.0705
  time to fit residues: 6.4338
Evaluate side-chains
  70 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 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 = 0.4311 r_free = 0.4311 target = 0.157186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.133660 restraints weight = 22174.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.140259 restraints weight = 10925.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.144503 restraints weight = 6290.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.147035 restraints weight = 4079.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.148992 restraints weight = 2959.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6287
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2773  Z= 0.129
  Angle     :  0.541   4.910   3760  Z= 0.296
  Chirality :  0.037   0.137    433
  Planarity :  0.005   0.041    459
  Dihedral  :  4.502  16.502    373
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 17.19 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.47), residues: 349
  helix:  1.08 (0.32), residues: 265
  sheet:  None (None), residues: 0
  loop : -1.86 (0.74), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 371 
 TYR   0.008   0.001   TYR A 201 
 PHE   0.008   0.001   PHE A 182 
 TRP   0.005   0.001   TRP A 109 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 2773)
  covalent geometry    : angle       0.54117 ( 3760)
  hydrogen bonds       : bond        0.03713 (  197)
  hydrogen bonds       : angle       5.29017 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8075 (mmp) cc_final: 0.7761 (mmp)
REVERT: A  274 MET cc_start: 0.8813 (ttp) cc_final: 0.7883 (tpp)
REVERT: A  403 MET cc_start: 0.5685 (tpp) cc_final: 0.5444 (tpp)
REVERT: A  408 ARG cc_start: 0.6846 (mtp85) cc_final: 0.6050 (tpt170)
  outliers start: 2
  outliers final: 2
  residues processed: 69
  average time/residue: 0.0781
  time to fit residues: 6.8203
Evaluate side-chains
  69 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 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 = 0.4296 r_free = 0.4296 target = 0.155726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.132181 restraints weight = 22135.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.138685 restraints weight = 10898.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.142947 restraints weight = 6302.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.145661 restraints weight = 4117.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.147324 restraints weight = 2934.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6346
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2773  Z= 0.170
  Angle     :  0.578   5.802   3760  Z= 0.323
  Chirality :  0.038   0.136    433
  Planarity :  0.005   0.037    459
  Dihedral  :  4.610  15.714    373
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 17.54 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.46), residues: 349
  helix:  0.82 (0.32), residues: 266
  sheet:  None (None), residues: 0
  loop : -2.02 (0.73), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 371 
 TYR   0.011   0.001   TYR A 201 
 PHE   0.013   0.001   PHE A 224 
 TRP   0.008   0.001   TRP A 109 
 HIS   0.003   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 2773)
  covalent geometry    : angle       0.57766 ( 3760)
  hydrogen bonds       : bond        0.03896 (  197)
  hydrogen bonds       : angle       5.47100 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8102 (mmp) cc_final: 0.7805 (mmp)
REVERT: A  274 MET cc_start: 0.8786 (ttp) cc_final: 0.7840 (tpp)
REVERT: A  403 MET cc_start: 0.5635 (tpp) cc_final: 0.5400 (tpp)
REVERT: A  408 ARG cc_start: 0.6799 (mtp85) cc_final: 0.6007 (tpt170)
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0690
  time to fit residues: 6.0943
Evaluate side-chains
  71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4300 r_free = 0.4300 target = 0.156172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.132667 restraints weight = 21875.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.139059 restraints weight = 10696.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.143348 restraints weight = 6214.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.145987 restraints weight = 4064.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.147837 restraints weight = 2909.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6321
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2773  Z= 0.154
  Angle     :  0.566   4.811   3760  Z= 0.313
  Chirality :  0.038   0.136    433
  Planarity :  0.004   0.037    459
  Dihedral  :  4.602  17.207    373
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 17.89 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.47), residues: 349
  helix:  0.84 (0.32), residues: 266
  sheet:  None (None), residues: 0
  loop : -1.98 (0.74), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.008   0.001   TYR A 201 
 PHE   0.011   0.001   PHE A 224 
 TRP   0.006   0.001   TRP A 324 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 2773)
  covalent geometry    : angle       0.56636 ( 3760)
  hydrogen bonds       : bond        0.03805 (  197)
  hydrogen bonds       : angle       5.42100 (  591)

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

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

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  698 Ramachandran restraints generated.
    349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8108 (mmp) cc_final: 0.7808 (mmp)
REVERT: A  274 MET cc_start: 0.8775 (ttp) cc_final: 0.7810 (tpp)
REVERT: A  403 MET cc_start: 0.5628 (tpp) cc_final: 0.5383 (tpp)
REVERT: A  408 ARG cc_start: 0.6793 (mtp85) cc_final: 0.6014 (tpt170)
  outliers start: 3
  outliers final: 3
  residues processed: 73
  average time/residue: 0.0786
  time to fit residues: 7.3253
Evaluate side-chains
  70 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  402 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 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 = 0.4315 r_free = 0.4315 target = 0.157274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.133990 restraints weight = 21843.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.140375 restraints weight = 10639.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.144669 restraints weight = 6165.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.147340 restraints weight = 4014.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.149157 restraints weight = 2857.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.4220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6292
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2773  Z= 0.126
  Angle     :  0.551   4.760   3760  Z= 0.300
  Chirality :  0.037   0.136    433
  Planarity :  0.005   0.039    459
  Dihedral  :  4.459  16.237    373
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 17.89 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.47), residues: 349
  helix:  1.07 (0.32), residues: 266
  sheet:  None (None), residues: 0
  loop : -1.87 (0.76), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 371 
 TYR   0.011   0.001   TYR A 201 
 PHE   0.010   0.001   PHE A 199 
 TRP   0.006   0.001   TRP A 109 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 2773)
  covalent geometry    : angle       0.55145 ( 3760)
  hydrogen bonds       : bond        0.03691 (  197)
  hydrogen bonds       : angle       5.26759 (  591)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1162.56 seconds
wall clock time: 20 minutes 22.24 seconds (1222.24 seconds total)