Starting phenix.real_space_refine
on Fri Aug 22 20:04:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bi9_44577/08_2025/9bi9_44577.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bi9_44577/08_2025/9bi9_44577.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bi9_44577/08_2025/9bi9_44577.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bi9_44577/08_2025/9bi9_44577.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bi9_44577/08_2025/9bi9_44577.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bi9_44577/08_2025/9bi9_44577.cif"
  }
  resolution = 2.61
  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=   0.006
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: 6
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      21      5.16       5
     C    2457      2.51       5
     N     663      2.21       5
     O     724      1.98       5
     H    3712      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 7578
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 7577
          Classifications: {'peptide': 497}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 39, 'TRANS': 457}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.38, per 1000 atoms: 0.18
  Number of scatterers: 7578
  At special positions: 0
  Unit cell: (67.32, 77.88, 77.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     Mg      1     11.99
     O     724      8.00
     N     663      7.00
     C    2457      6.00
     H    3712      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: 0.56
  Conformation dependent library (CDL) restraints added in 334.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  922

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 6 sheets defined
      48.3% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 68
    Processing helix  chain 'A' and resid 69 through 72
    Processing helix  chain 'A' and resid 79 through 98
      removed outlier: 3.810A  pdb=" N   ALA A  85 " --> pdb=" O   ASN A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 113
      removed outlier: 3.723A  pdb=" N   LEU A 113 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 3.518A  pdb=" N   TRP A 131 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 154
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 188 through 209
      removed outlier: 5.878A  pdb=" N   GLY A 201 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   LEU A 202 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 233
      Proline residue:  A 226  - end of helix
      removed outlier: 3.870A  pdb=" N   GLU A 230 " --> pdb=" O   PRO A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 250
    Processing helix  chain 'A' and resid 251 through 266
    Processing helix  chain 'A' and resid 268 through 281
      removed outlier: 4.226A  pdb=" N   ILE A 274 " --> pdb=" O   HIS A 270 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL A 275 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 325
    Processing helix  chain 'A' and resid 328 through 335
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 407 through 414
      removed outlier: 3.529A  pdb=" N   GLN A 414 " --> pdb=" O   SER A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 448
    Processing helix  chain 'A' and resid 451 through 469
      removed outlier: 3.520A  pdb=" N   GLU A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLY A 469 " --> pdb=" O   GLU A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 488
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
      removed outlier: 6.542A  pdb=" N   GLN A 291 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 30
      removed outlier: 5.327A  pdb=" N   LYS A  27 " --> pdb=" O   GLY A 420 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43
    Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337
    Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 341
      removed outlier: 4.270A  pdb=" N   ASP A 344 " --> pdb=" O   TYR A 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 390

    190 hydrogen bonds defined for protein.
    531 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: 1.38

  Time building geometry restraints manager: 0.85 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: 3705
        1.03 -     1.23: 7
        1.23 -     1.42: 1639
        1.42 -     1.61: 2294
        1.61 -     1.81: 35
  Bond restraints: 7680
  Sorted by residual:
  bond pdb=" CA  VAL A 179 "
       pdb=" CB  VAL A 179 "
    ideal  model  delta    sigma   weight residual
    1.538  1.514  0.024 9.80e-03 1.04e+04 6.18e+00
  bond pdb=" CA  ILE A 431 "
       pdb=" CB  ILE A 431 "
    ideal  model  delta    sigma   weight residual
    1.546  1.536  0.010 8.80e-03 1.29e+04 1.36e+00
  bond pdb=" CA  THR A 117 "
       pdb=" CB  THR A 117 "
    ideal  model  delta    sigma   weight residual
    1.529  1.514  0.015 1.61e-02 3.86e+03 8.85e-01
  bond pdb=" CA  GLU A 152 "
       pdb=" CB  GLU A 152 "
    ideal  model  delta    sigma   weight residual
    1.528  1.517  0.012 1.56e-02 4.11e+03 5.50e-01
  bond pdb=" CA  ASN A  81 "
       pdb=" CB  ASN A  81 "
    ideal  model  delta    sigma   weight residual
    1.529  1.518  0.012 1.74e-02 3.30e+03 4.41e-01
  ... (remaining 7675 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 12800
        0.99 -     1.97: 1005
        1.97 -     2.96: 40
        2.96 -     3.94: 30
        3.94 -     4.93: 9
  Bond angle restraints: 13884
  Sorted by residual:
  angle pdb=" CA  GLU A 152 "
        pdb=" CB  GLU A 152 "
        pdb=" CG  GLU A 152 "
      ideal   model   delta    sigma   weight residual
     114.10  109.17    4.93 2.00e+00 2.50e-01 6.07e+00
  angle pdb=" CB  GLU A 152 "
        pdb=" CG  GLU A 152 "
        pdb=" CD  GLU A 152 "
      ideal   model   delta    sigma   weight residual
     112.60  109.45    3.15 1.70e+00 3.46e-01 3.44e+00
  angle pdb=" N   ILE A 346 "
        pdb=" CA  ILE A 346 "
        pdb=" C   ILE A 346 "
      ideal   model   delta    sigma   weight residual
     109.34  106.02    3.32 2.08e+00 2.31e-01 2.54e+00
  angle pdb=" N   SER A 339 "
        pdb=" CA  SER A 339 "
        pdb=" C   SER A 339 "
      ideal   model   delta    sigma   weight residual
     110.80  107.42    3.38 2.13e+00 2.20e-01 2.52e+00
  angle pdb=" CA  ILE A 431 "
        pdb=" C   ILE A 431 "
        pdb=" N   PRO A 432 "
      ideal   model   delta    sigma   weight residual
     117.57  119.07   -1.50 1.01e+00 9.80e-01 2.20e+00
  ... (remaining 13879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.43: 3298
       16.43 -    32.86: 242
       32.86 -    49.29: 87
       49.29 -    65.72: 29
       65.72 -    82.16: 6
  Dihedral angle restraints: 3662
    sinusoidal: 1992
      harmonic: 1670
  Sorted by residual:
  dihedral pdb=" CA  HIS A 121 "
           pdb=" C   HIS A 121 "
           pdb=" N   PRO A 122 "
           pdb=" CA  PRO A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.03  -16.97     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  GLU A 364 "
           pdb=" C   GLU A 364 "
           pdb=" N   TYR A 365 "
           pdb=" CA  TYR A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.48   16.52     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ALA A 198 "
           pdb=" C   ALA A 198 "
           pdb=" N   PHE A 199 "
           pdb=" CA  PHE A 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.73  -15.27     0      5.00e+00 4.00e-02 9.32e+00
  ... (remaining 3659 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 364
       0.026 -    0.053: 139
       0.053 -    0.079: 41
       0.079 -    0.105: 32
       0.105 -    0.131: 10
  Chirality restraints: 586
  Sorted by residual:
  chirality pdb=" CA  ILE A 346 "
            pdb=" N   ILE A 346 "
            pdb=" C   ILE A 346 "
            pdb=" CB  ILE A 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE A 294 "
            pdb=" N   ILE A 294 "
            pdb=" C   ILE A 294 "
            pdb=" CB  ILE A 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  PRO A 122 "
            pdb=" N   PRO A 122 "
            pdb=" C   PRO A 122 "
            pdb=" CB  PRO A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 583 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 371 "   -0.046 5.00e-02 4.00e+02   7.04e-02 7.93e+00
        pdb=" N   PRO A 372 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 372 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 372 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 225 "   -0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO A 226 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 226 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 226 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 137 "   -0.005 2.00e-02 2.50e+03   1.05e-02 1.10e+00
        pdb=" C   THR A 137 "    0.018 2.00e-02 2.50e+03
        pdb=" O   THR A 137 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY A 138 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 428
        2.21 -     2.80: 15241
        2.80 -     3.40: 19973
        3.40 -     4.00: 25580
        4.00 -     4.60: 39737
  Nonbonded interactions: 100959
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 246 "
            pdb="HE21 GLN A 250 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" O   PHE A  28 "
            pdb=" HE2 HIS A 423 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" O   SER A 118 "
            pdb=" HZ1 LYS A 127 "
     model   vdw
     1.617 2.450
  nonbonded pdb="HD21 ASN A 220 "
            pdb=" OE2 GLU A 223 "
     model   vdw
     1.624 2.450
  nonbonded pdb="HH12 ARG A  74 "
            pdb=" O   SER A 248 "
     model   vdw
     1.650 2.450
  ... (remaining 100954 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=0.50 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:             1.590
  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:             0.060
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.150
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
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   0.024   3968  Z= 0.130
  Angle     :  0.528   4.929   5393  Z= 0.264
  Chirality :  0.038   0.131    586
  Planarity :  0.004   0.070    700
  Dihedral  : 12.519  82.156   1477
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.39), residues: 495
  helix:  2.16 (0.37), residues: 212
  sheet: -1.30 (0.68), residues: 53
  loop : -0.52 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 216 
 TYR   0.007   0.001   TYR A 239 
 PHE   0.005   0.001   PHE A 265 
 TRP   0.006   0.001   TRP A  29 
 HIS   0.004   0.001   HIS A 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3968)
  covalent geometry    : angle       0.52778 ( 5393)
  hydrogen bonds       : bond        0.14153 (  190)
  hydrogen bonds       : angle       6.17145 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9190 (tp40) cc_final: 0.8990 (tm-30)
REVERT: A  149 LEU cc_start: 0.9270 (tt) cc_final: 0.9053 (tp)
REVERT: A  157 MET cc_start: 0.7865 (mtp) cc_final: 0.7483 (mtp)
REVERT: A  207 LYS cc_start: 0.7473 (tmmt) cc_final: 0.7209 (ttmm)
REVERT: A  242 ASP cc_start: 0.8289 (t70) cc_final: 0.7943 (t0)
REVERT: A  392 ARG cc_start: 0.8368 (mtm110) cc_final: 0.8053 (mtm-85)
REVERT: A  396 THR cc_start: 0.8619 (m) cc_final: 0.8344 (p)
REVERT: A  475 VAL cc_start: 0.9187 (m) cc_final: 0.8886 (m)
  outliers start: 0
  outliers final: 1
  residues processed: 95
  average time/residue: 1.1106
  time to fit residues: 108.4937
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 250 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.099330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.079572 restraints weight = 20751.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 3.83
r_work: 0.3054 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3968  Z= 0.120
  Angle     :  0.573   4.633   5393  Z= 0.284
  Chirality :  0.038   0.129    586
  Planarity :  0.005   0.053    700
  Dihedral  :  3.985  15.718    537
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 10.77 %
    Favored  : 88.52 %
  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:  0.74 (0.38), residues: 495
  helix:  2.14 (0.37), residues: 215
  sheet: -1.40 (0.67), residues: 53
  loop : -0.64 (0.38), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 234 
 TYR   0.008   0.001   TYR A 239 
 PHE   0.009   0.001   PHE A 487 
 TRP   0.008   0.001   TRP A  29 
 HIS   0.004   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3968)
  covalent geometry    : angle       0.57335 ( 5393)
  hydrogen bonds       : bond        0.03835 (  190)
  hydrogen bonds       : angle       5.19365 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9341 (tp40) cc_final: 0.9122 (tm-30)
REVERT: A  207 LYS cc_start: 0.7730 (tmmt) cc_final: 0.7395 (ttmm)
REVERT: A  242 ASP cc_start: 0.8784 (t70) cc_final: 0.8502 (t0)
REVERT: A  496 ASP cc_start: 0.8811 (t0) cc_final: 0.8422 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 59
  average time/residue: 1.1169
  time to fit residues: 68.0048
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.093957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.074072 restraints weight = 20775.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 3.80
r_work: 0.2942 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3968  Z= 0.178
  Angle     :  0.577   4.531   5393  Z= 0.289
  Chirality :  0.040   0.126    586
  Planarity :  0.006   0.081    700
  Dihedral  :  4.035  15.439    535
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.16 %
    Favored  : 85.41 %
  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:  0.60 (0.38), residues: 495
  helix:  2.04 (0.36), residues: 213
  sheet: -1.71 (0.66), residues: 53
  loop : -0.63 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 392 
 TYR   0.009   0.001   TYR A   8 
 PHE   0.008   0.001   PHE A 403 
 TRP   0.008   0.001   TRP A  29 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 3968)
  covalent geometry    : angle       0.57653 ( 5393)
  hydrogen bonds       : bond        0.04160 (  190)
  hydrogen bonds       : angle       5.18921 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9363 (tp40) cc_final: 0.9115 (tm-30)
REVERT: A  207 LYS cc_start: 0.7718 (tmmt) cc_final: 0.7386 (ttmm)
REVERT: A  242 ASP cc_start: 0.8879 (t70) cc_final: 0.8568 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 55
  average time/residue: 1.0000
  time to fit residues: 56.9956
Evaluate side-chains
  49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  462 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.092799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.072975 restraints weight = 20969.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 3.81
r_work: 0.2934 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3968  Z= 0.152
  Angle     :  0.557   4.437   5393  Z= 0.278
  Chirality :  0.039   0.125    586
  Planarity :  0.006   0.053    700
  Dihedral  :  3.963  15.656    535
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.11 %
    Favored  : 84.69 %
  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:  0.63 (0.38), residues: 495
  helix:  2.05 (0.36), residues: 213
  sheet: -1.70 (0.69), residues: 53
  loop : -0.60 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 397 
 TYR   0.009   0.001   TYR A 455 
 PHE   0.007   0.001   PHE A 265 
 TRP   0.007   0.001   TRP A  29 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3968)
  covalent geometry    : angle       0.55717 ( 5393)
  hydrogen bonds       : bond        0.03812 (  190)
  hydrogen bonds       : angle       5.11537 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9365 (tp40) cc_final: 0.9119 (tm-30)
REVERT: A  207 LYS cc_start: 0.7721 (tmmt) cc_final: 0.7237 (mttp)
REVERT: A  221 MET cc_start: 0.7192 (mmt) cc_final: 0.6986 (mtt)
REVERT: A  242 ASP cc_start: 0.8926 (t70) cc_final: 0.8610 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 54
  average time/residue: 1.0544
  time to fit residues: 59.0270
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  462 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.091973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.072171 restraints weight = 20697.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 3.75
r_work: 0.2920 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3968  Z= 0.166
  Angle     :  0.562   4.805   5393  Z= 0.281
  Chirality :  0.039   0.125    586
  Planarity :  0.005   0.049    700
  Dihedral  :  3.946  15.499    535
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.35 %
    Favored  : 84.21 %
  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:  0.58 (0.38), residues: 495
  helix:  2.00 (0.36), residues: 214
  sheet: -1.68 (0.70), residues: 53
  loop : -0.64 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 477 
 TYR   0.012   0.001   TYR A 455 
 PHE   0.008   0.001   PHE A 265 
 TRP   0.006   0.001   TRP A  29 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3968)
  covalent geometry    : angle       0.56230 ( 5393)
  hydrogen bonds       : bond        0.03926 (  190)
  hydrogen bonds       : angle       5.12425 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9368 (tp40) cc_final: 0.9101 (tm-30)
REVERT: A  207 LYS cc_start: 0.7728 (tmmt) cc_final: 0.7253 (mttp)
REVERT: A  242 ASP cc_start: 0.8954 (t70) cc_final: 0.8621 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 52
  average time/residue: 1.0723
  time to fit residues: 57.8576
Evaluate side-chains
  49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  462 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.091543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.071863 restraints weight = 20806.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 3.75
r_work: 0.2927 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3968  Z= 0.167
  Angle     :  0.558   5.027   5393  Z= 0.279
  Chirality :  0.039   0.125    586
  Planarity :  0.005   0.054    700
  Dihedral  :  3.966  15.438    535
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.35 %
    Favored  : 84.45 %
  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:  0.58 (0.38), residues: 495
  helix:  2.02 (0.36), residues: 213
  sheet: -1.69 (0.69), residues: 53
  loop : -0.64 (0.38), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 477 
 TYR   0.014   0.001   TYR A 455 
 PHE   0.008   0.001   PHE A 265 
 TRP   0.007   0.001   TRP A 493 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3968)
  covalent geometry    : angle       0.55841 ( 5393)
  hydrogen bonds       : bond        0.03932 (  190)
  hydrogen bonds       : angle       5.13123 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9373 (tp40) cc_final: 0.9107 (tm-30)
REVERT: A  207 LYS cc_start: 0.7726 (tmmt) cc_final: 0.7230 (mttp)
REVERT: A  242 ASP cc_start: 0.8983 (t70) cc_final: 0.8646 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 53
  average time/residue: 0.9163
  time to fit residues: 50.4662
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  462 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.092219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.072453 restraints weight = 20750.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.78
r_work: 0.2941 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3968  Z= 0.128
  Angle     :  0.551   5.744   5393  Z= 0.273
  Chirality :  0.038   0.124    586
  Planarity :  0.005   0.057    700
  Dihedral  :  3.883  15.489    535
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.07 %
    Favored  : 83.73 %
  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:  0.72 (0.38), residues: 495
  helix:  2.14 (0.37), residues: 213
  sheet: -1.68 (0.69), residues: 53
  loop : -0.56 (0.38), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 477 
 TYR   0.011   0.001   TYR A 455 
 PHE   0.007   0.001   PHE A 265 
 TRP   0.011   0.001   TRP A 493 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3968)
  covalent geometry    : angle       0.55088 ( 5393)
  hydrogen bonds       : bond        0.03620 (  190)
  hydrogen bonds       : angle       5.02751 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9366 (tp40) cc_final: 0.9102 (tm-30)
REVERT: A  207 LYS cc_start: 0.7723 (tmmt) cc_final: 0.7220 (mttp)
REVERT: A  242 ASP cc_start: 0.8979 (t70) cc_final: 0.8642 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 51
  average time/residue: 1.0380
  time to fit residues: 54.9438
Evaluate side-chains
  53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  462 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3382 r_free = 0.3382 target = 0.092380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.072532 restraints weight = 20889.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 3.82
r_work: 0.2931 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3968  Z= 0.118
  Angle     :  0.546   5.259   5393  Z= 0.270
  Chirality :  0.038   0.123    586
  Planarity :  0.005   0.061    700
  Dihedral  :  3.825  15.457    535
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 15.31 %
    Favored  : 83.73 %
  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:  0.77 (0.38), residues: 495
  helix:  2.20 (0.37), residues: 213
  sheet: -1.72 (0.68), residues: 56
  loop : -0.52 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 477 
 TYR   0.015   0.001   TYR A 455 
 PHE   0.009   0.001   PHE A 487 
 TRP   0.016   0.001   TRP A 493 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3968)
  covalent geometry    : angle       0.54604 ( 5393)
  hydrogen bonds       : bond        0.03478 (  190)
  hydrogen bonds       : angle       4.96925 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9369 (tp40) cc_final: 0.9097 (tm-30)
REVERT: A  207 LYS cc_start: 0.7703 (tmmt) cc_final: 0.7201 (mttp)
REVERT: A  242 ASP cc_start: 0.8976 (t70) cc_final: 0.8645 (t0)
REVERT: A  344 ASP cc_start: 0.8850 (m-30) cc_final: 0.8275 (m-30)
REVERT: A  419 ARG cc_start: 0.8749 (ptp-170) cc_final: 0.8545 (ptp-170)
  outliers start: 4
  outliers final: 3
  residues processed: 53
  average time/residue: 0.9667
  time to fit residues: 53.0233
Evaluate side-chains
  51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  462 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0030
   chunk 37 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.093306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.073804 restraints weight = 20585.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 3.78
r_work: 0.2966 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3968  Z= 0.105
  Angle     :  0.538   4.885   5393  Z= 0.266
  Chirality :  0.038   0.123    586
  Planarity :  0.005   0.064    700
  Dihedral  :  3.761  15.420    535
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.79 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.38), residues: 495
  helix:  2.07 (0.37), residues: 220
  sheet: -1.89 (0.75), residues: 44
  loop : -0.60 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 477 
 TYR   0.013   0.001   TYR A 455 
 PHE   0.006   0.001   PHE A 482 
 TRP   0.020   0.001   TRP A 493 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3968)
  covalent geometry    : angle       0.53834 ( 5393)
  hydrogen bonds       : bond        0.03258 (  190)
  hydrogen bonds       : angle       4.89045 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9368 (tp40) cc_final: 0.9100 (tm-30)
REVERT: A  207 LYS cc_start: 0.7678 (tmmt) cc_final: 0.7177 (mttp)
REVERT: A  242 ASP cc_start: 0.8994 (t70) cc_final: 0.8669 (t0)
REVERT: A  344 ASP cc_start: 0.8830 (m-30) cc_final: 0.8269 (m-30)
  outliers start: 3
  outliers final: 2
  residues processed: 54
  average time/residue: 1.1222
  time to fit residues: 62.7178
Evaluate side-chains
  49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  459 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   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 = 0.3398 r_free = 0.3398 target = 0.093349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.073734 restraints weight = 20699.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 3.81
r_work: 0.2957 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3968  Z= 0.110
  Angle     :  0.555   6.987   5393  Z= 0.272
  Chirality :  0.038   0.123    586
  Planarity :  0.005   0.062    700
  Dihedral  :  3.742  15.194    535
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.55 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.38), residues: 495
  helix:  2.07 (0.37), residues: 220
  sheet: -1.83 (0.76), residues: 44
  loop : -0.61 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 477 
 TYR   0.016   0.001   TYR A 455 
 PHE   0.011   0.001   PHE A 487 
 TRP   0.024   0.001   TRP A 493 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3968)
  covalent geometry    : angle       0.55524 ( 5393)
  hydrogen bonds       : bond        0.03303 (  190)
  hydrogen bonds       : angle       4.88215 (  531)

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

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

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  990 Ramachandran restraints generated.
    495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   21 is missing expected H atoms. Skipping.
Residue LYS   49 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue MET  471 is missing expected H atoms. Skipping.
Evaluate side-chains
  55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9365 (tp40) cc_final: 0.9098 (tm-30)
REVERT: A  207 LYS cc_start: 0.7684 (tmmt) cc_final: 0.7352 (ttmm)
REVERT: A  242 ASP cc_start: 0.8999 (t70) cc_final: 0.8682 (t0)
REVERT: A  344 ASP cc_start: 0.8823 (m-30) cc_final: 0.8263 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 54
  average time/residue: 0.9206
  time to fit residues: 51.6999
Evaluate side-chains
  51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  459 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0170
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.1222

-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.092447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.072745 restraints weight = 20562.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 3.79
r_work: 0.2944 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3968  Z= 0.132
  Angle     :  0.563   5.961   5393  Z= 0.281
  Chirality :  0.039   0.123    586
  Planarity :  0.005   0.063    700
  Dihedral  :  3.754  15.197    535
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.79 %
    Favored  : 82.78 %
  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:  0.66 (0.38), residues: 495
  helix:  2.06 (0.37), residues: 220
  sheet: -1.82 (0.77), residues: 44
  loop : -0.69 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 477 
 TYR   0.016   0.001   TYR A 455 
 PHE   0.008   0.001   PHE A 265 
 TRP   0.023   0.001   TRP A 493 
 HIS   0.003   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3968)
  covalent geometry    : angle       0.56296 ( 5393)
  hydrogen bonds       : bond        0.03455 (  190)
  hydrogen bonds       : angle       4.92716 (  531)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2991.72 seconds
wall clock time: 51 minutes 17.10 seconds (3077.10 seconds total)