Starting phenix.real_space_refine
on Mon Jan 13 19:27:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
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
     Mn      1      7.51       5
     S      21      5.16       5
     C    2416      2.51       5
     N     591      2.21       5
     O     623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3652
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3651
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 16, 'TRANS': 454}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.47, per 1000 atoms: 0.68
  Number of scatterers: 3652
  At special positions: 0
  Unit cell: (83.328, 67.704, 70.308, 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)
     Mn      1     24.99
     S      21     16.00
     O     623      8.00
     N     591      7.00
     C    2416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 394 " distance=2.04

  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: 0.86
  Conformation dependent library (CDL) restraints added in 459.0 milliseconds
  

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  864

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      87.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 102
      removed outlier: 3.832A  pdb=" N   ALA A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 113
      removed outlier: 4.281A  pdb=" N   LEU A 108 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR A 113 " --> pdb=" O   MET A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 129
      removed outlier: 3.624A  pdb=" N   ALA A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
      removed outlier: 3.836A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 130 through 133'
    Processing helix  chain 'A' and resid 134 through 158
      removed outlier: 3.570A  pdb=" N   LEU A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 170
    Processing helix  chain 'A' and resid 171 through 205
      removed outlier: 3.522A  pdb=" N   ARG A 175 " --> pdb=" O   PRO A 171 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE A 177 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'A' and resid 219 through 232
      removed outlier: 3.809A  pdb=" N   PHE A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 259
    Processing helix  chain 'A' and resid 261 through 271
    Processing helix  chain 'A' and resid 278 through 293
      removed outlier: 4.097A  pdb=" N   ILE A 293 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 3.597A  pdb=" N   LEU A 300 " --> pdb=" O   HIS A 296 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 352
      removed outlier: 3.642A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 367
      removed outlier: 3.560A  pdb=" N   VAL A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 430
      removed outlier: 3.557A  pdb=" N   GLY A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      Proline residue:  A 398  - end of helix
      removed outlier: 3.758A  pdb=" N   LEU A 401 " --> pdb=" O   GLY A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 459
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 460 through 479
    Processing helix  chain 'A' and resid 479 through 490
      Proline residue:  A 485  - end of helix
    Processing helix  chain 'A' and resid 492 through 497
    Processing helix  chain 'A' and resid 502 through 532
      removed outlier: 3.952A  pdb=" N   ASP A 530 " --> pdb=" O   VAL A 526 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LEU A 531 " --> pdb=" O   TYR A 527 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY A 532 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 562

    293 hydrogen bonds defined for protein.
    879 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: 0.97

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1117
        1.35 -     1.47: 936
        1.47 -     1.59: 1651
        1.59 -     1.71: 2
        1.71 -     1.83: 33
  Bond restraints: 3739
  Sorted by residual:
  bond pdb=" CA  PHE A 239 "
       pdb=" C   PHE A 239 "
    ideal  model  delta    sigma   weight residual
    1.524  1.485  0.039 1.27e-02 6.20e+03 9.46e+00
  bond pdb=" CB  ILE A 327 "
       pdb=" CG2 ILE A 327 "
    ideal  model  delta    sigma   weight residual
    1.521  1.604 -0.083 3.30e-02 9.18e+02 6.27e+00
  bond pdb=" CB  ILE A 519 "
       pdb=" CG2 ILE A 519 "
    ideal  model  delta    sigma   weight residual
    1.521  1.597 -0.076 3.30e-02 9.18e+02 5.24e+00
  bond pdb=" N   TYR A 527 "
       pdb=" CA  TYR A 527 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.33e-02 5.65e+03 4.48e+00
  bond pdb=" CB  ILE A 288 "
       pdb=" CG1 ILE A 288 "
    ideal  model  delta    sigma   weight residual
    1.530  1.572 -0.042 2.00e-02 2.50e+03 4.38e+00
  ... (remaining 3734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 4724
        2.06 -     4.11: 280
        4.11 -     6.17: 58
        6.17 -     8.23: 24
        8.23 -    10.28: 3
  Bond angle restraints: 5089
  Sorted by residual:
  angle pdb=" C   LEU A 228 "
        pdb=" N   ASP A 229 "
        pdb=" CA  ASP A 229 "
      ideal   model   delta    sigma   weight residual
     120.44  113.90    6.54 1.30e+00 5.92e-01 2.53e+01
  angle pdb=" N   LEU A 145 "
        pdb=" CA  LEU A 145 "
        pdb=" C   LEU A 145 "
      ideal   model   delta    sigma   weight residual
     111.07  106.69    4.38 1.07e+00 8.73e-01 1.67e+01
  angle pdb=" N   PHE A 239 "
        pdb=" CA  PHE A 239 "
        pdb=" C   PHE A 239 "
      ideal   model   delta    sigma   weight residual
     111.07  106.72    4.35 1.07e+00 8.73e-01 1.65e+01
  angle pdb=" C   ASN A 297 "
        pdb=" N   MET A 298 "
        pdb=" CA  MET A 298 "
      ideal   model   delta    sigma   weight residual
     120.65  115.46    5.19 1.32e+00 5.74e-01 1.55e+01
  angle pdb=" N   ASP A 229 "
        pdb=" CA  ASP A 229 "
        pdb=" C   ASP A 229 "
      ideal   model   delta    sigma   weight residual
     111.07  106.89    4.18 1.07e+00 8.73e-01 1.53e+01
  ... (remaining 5084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 1890
       17.20 -    34.39: 200
       34.39 -    51.58: 56
       51.58 -    68.78: 12
       68.78 -    85.97: 6
  Dihedral angle restraints: 2164
    sinusoidal: 814
      harmonic: 1350
  Sorted by residual:
  dihedral pdb=" CB  CYS A 363 "
           pdb=" SG  CYS A 363 "
           pdb=" SG  CYS A 394 "
           pdb=" CB  CYS A 394 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.95   55.05     1      1.00e+01 1.00e-02 4.10e+01
  dihedral pdb=" CA  ASP A 469 "
           pdb=" CB  ASP A 469 "
           pdb=" CG  ASP A 469 "
           pdb=" OD1 ASP A 469 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.68   59.68     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CA  THR A 490 "
           pdb=" C   THR A 490 "
           pdb=" N   SER A 491 "
           pdb=" CA  SER A 491 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.89   17.11     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 2161 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 406
       0.045 -    0.090: 142
       0.090 -    0.135: 36
       0.135 -    0.179: 12
       0.179 -    0.224: 7
  Chirality restraints: 603
  Sorted by residual:
  chirality pdb=" CG  LEU A 249 "
            pdb=" CB  LEU A 249 "
            pdb=" CD1 LEU A 249 "
            pdb=" CD2 LEU A 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  VAL A 442 "
            pdb=" CA  VAL A 442 "
            pdb=" CG1 VAL A 442 "
            pdb=" CG2 VAL A 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.84    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  ILE A 447 "
            pdb=" CA  ILE A 447 "
            pdb=" CG1 ILE A 447 "
            pdb=" CG2 ILE A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 600 not shown)

  Planarity restraints: 627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 279 "    0.059 5.00e-02 4.00e+02   8.94e-02 1.28e+01
        pdb=" N   PRO A 280 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A 280 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 280 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 297 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.50e+00
        pdb=" C   ASN A 297 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASN A 297 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 298 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 104 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.30e+00
        pdb=" N   PRO A 105 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "    0.032 5.00e-02 4.00e+02
  ... (remaining 624 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.50: 16
        2.50 -     3.10: 2690
        3.10 -     3.70: 5756
        3.70 -     4.30: 7655
        4.30 -     4.90: 12775
  Nonbonded interactions: 28892
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 376 "
            pdb=" OD1 ASP A 377 "
     model   vdw
     1.906 3.040
  nonbonded pdb=" OD2 ASP A 115 "
            pdb="MN    MN A 701 "
     model   vdw
     2.159 2.320
  nonbonded pdb=" O   VAL A 215 "
            pdb=" OG1 THR A 218 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   LEU A 514 "
            pdb=" OG  SER A 518 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER A 491 "
            pdb=" OD1 ASN A 501 "
     model   vdw
     2.306 3.040
  ... (remaining 28887 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:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.083   3739  Z= 0.497
  Angle     :  1.195  10.281   5089  Z= 0.627
  Chirality :  0.054   0.224    603
  Planarity :  0.008   0.089    627
  Dihedral  : 16.583  85.972   1297
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.41 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.34), residues: 469
  helix: -0.07 (0.23), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.69 (0.64), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 135 
 HIS   0.006   0.002   HIS A 161 
 PHE   0.028   0.002   PHE A 347 
 TYR   0.033   0.002   TYR A 324 
 ARG   0.012   0.001   ARG A 440 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7953 (mp0)
REVERT: A  305 VAL cc_start: 0.8895 (t) cc_final: 0.8601 (m)
REVERT: A  471 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8427 (mp)
REVERT: A  476 SER cc_start: 0.8750 (t) cc_final: 0.8168 (p)
REVERT: A  521 MET cc_start: 0.8345 (ttp) cc_final: 0.8027 (mtp)
REVERT: A  537 TYR cc_start: 0.7734 (t80) cc_final: 0.7362 (t80)
REVERT: A  552 PHE cc_start: 0.8790 (m-10) cc_final: 0.8204 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1038
  time to fit residues: 16.5321
Evaluate side-chains
  108 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  518 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.127540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.105283 restraints weight = 5849.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109001 restraints weight = 3009.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111533 restraints weight = 1962.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3739  Z= 0.210
  Angle     :  0.592   9.811   5089  Z= 0.303
  Chirality :  0.038   0.140    603
  Planarity :  0.005   0.060    627
  Dihedral  :  6.269  58.205    517
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 21.88 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.37), residues: 469
  helix:  1.46 (0.25), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.50 (0.65), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 556 
 HIS   0.004   0.001   HIS A 296 
 PHE   0.016   0.001   PHE A 438 
 TYR   0.010   0.001   TYR A 547 
 ARG   0.006   0.001   ARG A 440 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ASN cc_start: 0.9009 (m-40) cc_final: 0.8724 (m-40)
REVERT: A  148 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.6741 (mp10)
REVERT: A  158 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8789 (p)
REVERT: A  305 VAL cc_start: 0.9167 (t) cc_final: 0.8854 (m)
REVERT: A  345 SER cc_start: 0.9195 (t) cc_final: 0.8813 (p)
REVERT: A  476 SER cc_start: 0.8648 (t) cc_final: 0.8166 (p)
REVERT: A  477 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8891 (tp)
REVERT: A  521 MET cc_start: 0.8471 (ttp) cc_final: 0.8180 (mtp)
REVERT: A  552 PHE cc_start: 0.8863 (m-10) cc_final: 0.8382 (m-80)
  outliers start: 23
  outliers final: 9
  residues processed: 108
  average time/residue: 0.1013
  time to fit residues: 15.0658
Evaluate side-chains
  105 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 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 = 0.3496 r_free = 0.3496 target = 0.127493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.104932 restraints weight = 5811.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.108593 restraints weight = 3082.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.110906 restraints weight = 2048.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3739  Z= 0.179
  Angle     :  0.591  12.474   5089  Z= 0.290
  Chirality :  0.037   0.113    603
  Planarity :  0.005   0.057    627
  Dihedral  :  5.664  57.615    510
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 23.66 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.38), residues: 469
  helix:  2.01 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.45 (0.66), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 296 
 PHE   0.018   0.001   PHE A 347 
 TYR   0.014   0.001   TYR A 547 
 ARG   0.002   0.000   ARG A 440 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ASN cc_start: 0.8948 (m-40) cc_final: 0.8607 (m110)
REVERT: A  148 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.6749 (mp10)
REVERT: A  158 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8630 (p)
REVERT: A  249 LEU cc_start: 0.8710 (mm) cc_final: 0.8493 (mm)
REVERT: A  305 VAL cc_start: 0.9217 (t) cc_final: 0.8959 (m)
REVERT: A  345 SER cc_start: 0.9188 (t) cc_final: 0.8763 (p)
REVERT: A  476 SER cc_start: 0.8636 (t) cc_final: 0.8172 (p)
REVERT: A  537 TYR cc_start: 0.7744 (t80) cc_final: 0.7228 (t80)
REVERT: A  552 PHE cc_start: 0.8890 (m-10) cc_final: 0.8418 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1052
  time to fit residues: 15.2358
Evaluate side-chains
  106 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.126432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.103392 restraints weight = 5962.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.107003 restraints weight = 3158.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.109338 restraints weight = 2097.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3739  Z= 0.214
  Angle     :  0.600  11.330   5089  Z= 0.297
  Chirality :  0.038   0.162    603
  Planarity :  0.004   0.057    627
  Dihedral  :  5.579  59.457    508
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 23.41 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.39), residues: 469
  helix:  2.06 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.25 (0.68), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.020   0.001   PHE A 347 
 TYR   0.011   0.001   TYR A 547 
 ARG   0.005   0.000   ARG A 440 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.6595 (mp10)
REVERT: A  158 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (p)
REVERT: A  249 LEU cc_start: 0.8710 (mm) cc_final: 0.8506 (mm)
REVERT: A  305 VAL cc_start: 0.9199 (t) cc_final: 0.8931 (m)
REVERT: A  345 SER cc_start: 0.9186 (t) cc_final: 0.8814 (p)
REVERT: A  476 SER cc_start: 0.8597 (t) cc_final: 0.8153 (p)
REVERT: A  537 TYR cc_start: 0.7748 (t80) cc_final: 0.7234 (t80)
REVERT: A  552 PHE cc_start: 0.8843 (m-10) cc_final: 0.8398 (m-80)
  outliers start: 29
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1023
  time to fit residues: 15.5058
Evaluate side-chains
  103 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    0.3980
   chunk 43 optimal weight:    0.0870
   chunk 10 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.128685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.105832 restraints weight = 6034.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.109539 restraints weight = 3181.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111892 restraints weight = 2104.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3739  Z= 0.183
  Angle     :  0.604  12.979   5089  Z= 0.294
  Chirality :  0.038   0.144    603
  Planarity :  0.004   0.057    627
  Dihedral  :  5.384  57.578    508
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 24.43 %
    Favored  : 68.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.39), residues: 469
  helix:  2.16 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.26 (0.66), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 296 
 PHE   0.020   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 547 
 ARG   0.004   0.000   ARG A 440 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.6747 (mp10)
REVERT: A  158 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.7957 (m)
REVERT: A  294 MET cc_start: 0.7833 (mmm) cc_final: 0.7593 (mmm)
REVERT: A  305 VAL cc_start: 0.9149 (t) cc_final: 0.8881 (m)
REVERT: A  345 SER cc_start: 0.9242 (t) cc_final: 0.8834 (p)
REVERT: A  476 SER cc_start: 0.8672 (t) cc_final: 0.8167 (p)
REVERT: A  537 TYR cc_start: 0.8016 (t80) cc_final: 0.7494 (t80)
REVERT: A  552 PHE cc_start: 0.8870 (m-10) cc_final: 0.8410 (m-80)
  outliers start: 28
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1108
  time to fit residues: 16.2649
Evaluate side-chains
  110 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0370
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 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 = 0.3488 r_free = 0.3488 target = 0.127096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.104307 restraints weight = 6045.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.107907 restraints weight = 3156.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110464 restraints weight = 2087.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3739  Z= 0.193
  Angle     :  0.621  11.767   5089  Z= 0.301
  Chirality :  0.038   0.141    603
  Planarity :  0.004   0.056    627
  Dihedral  :  5.356  58.390    508
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 25.45 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.39), residues: 469
  helix:  2.14 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.23 (0.69), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 435 
 HIS   0.002   0.001   HIS A 296 
 PHE   0.018   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 553 
 ARG   0.002   0.000   ARG A 445 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.9005 (m-80) cc_final: 0.8381 (m-80)
REVERT: A  148 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.6438 (mp10)
REVERT: A  158 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.7853 (m)
REVERT: A  305 VAL cc_start: 0.9177 (t) cc_final: 0.8909 (m)
REVERT: A  345 SER cc_start: 0.9221 (t) cc_final: 0.8820 (p)
REVERT: A  476 SER cc_start: 0.8670 (t) cc_final: 0.8178 (p)
REVERT: A  537 TYR cc_start: 0.8079 (t80) cc_final: 0.7586 (t80)
REVERT: A  552 PHE cc_start: 0.8855 (m-10) cc_final: 0.8384 (m-80)
  outliers start: 29
  outliers final: 17
  residues processed: 116
  average time/residue: 0.1123
  time to fit residues: 17.3645
Evaluate side-chains
  110 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0020
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.126347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.103595 restraints weight = 6009.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.107116 restraints weight = 3213.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.109627 restraints weight = 2147.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3739  Z= 0.200
  Angle     :  0.659  10.762   5089  Z= 0.315
  Chirality :  0.042   0.331    603
  Planarity :  0.004   0.054    627
  Dihedral  :  5.350  58.701    508
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 26.46 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.39), residues: 469
  helix:  2.10 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.08 (0.70), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 435 
 HIS   0.002   0.001   HIS A 296 
 PHE   0.017   0.001   PHE A 347 
 TYR   0.009   0.001   TYR A 547 
 ARG   0.005   0.000   ARG A 278 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.6433 (mp10)
REVERT: A  158 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.7808 (m)
REVERT: A  305 VAL cc_start: 0.9247 (t) cc_final: 0.9034 (m)
REVERT: A  345 SER cc_start: 0.9213 (t) cc_final: 0.8837 (p)
REVERT: A  363 CYS cc_start: 0.5943 (t) cc_final: 0.5417 (t)
REVERT: A  476 SER cc_start: 0.8627 (t) cc_final: 0.8154 (p)
REVERT: A  537 TYR cc_start: 0.8086 (t80) cc_final: 0.7562 (t80)
REVERT: A  552 PHE cc_start: 0.8908 (m-10) cc_final: 0.8459 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 108
  average time/residue: 0.1052
  time to fit residues: 15.2055
Evaluate side-chains
  111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0870
   chunk 4 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 148 GLN
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.126783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.104785 restraints weight = 5997.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.108330 restraints weight = 3145.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.110833 restraints weight = 2074.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3739  Z= 0.207
  Angle     :  0.681  13.230   5089  Z= 0.321
  Chirality :  0.042   0.331    603
  Planarity :  0.004   0.055    627
  Dihedral  :  5.338  58.393    508
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 26.46 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.39), residues: 469
  helix:  2.09 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.07 (0.69), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 435 
 HIS   0.001   0.001   HIS A 161 
 PHE   0.007   0.001   PHE A 438 
 TYR   0.009   0.001   TYR A 547 
 ARG   0.002   0.000   ARG A 440 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  122 ASP cc_start: 0.8244 (m-30) cc_final: 0.8038 (m-30)
REVERT: A  158 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.7829 (m)
REVERT: A  305 VAL cc_start: 0.9244 (t) cc_final: 0.9017 (m)
REVERT: A  476 SER cc_start: 0.8642 (t) cc_final: 0.8157 (p)
REVERT: A  537 TYR cc_start: 0.8132 (t80) cc_final: 0.7623 (t80)
  outliers start: 28
  outliers final: 23
  residues processed: 110
  average time/residue: 0.0969
  time to fit residues: 14.6369
Evaluate side-chains
  112 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  559 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 8 optimal weight:    0.0770
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 192 GLN
A 281 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.124982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.102565 restraints weight = 5966.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.106161 restraints weight = 3145.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.108473 restraints weight = 2070.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3739  Z= 0.223
  Angle     :  0.710  13.356   5089  Z= 0.335
  Chirality :  0.044   0.355    603
  Planarity :  0.005   0.054    627
  Dihedral  :  5.397  58.894    508
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  7.63 %
    Allowed  : 26.21 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.39), residues: 469
  helix:  2.05 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.07 (0.69), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 135 
 HIS   0.002   0.001   HIS A 161 
 PHE   0.010   0.001   PHE A 523 
 TYR   0.009   0.001   TYR A 547 
 ARG   0.015   0.001   ARG A 278 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A  158 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7646 (m)
REVERT: A  305 VAL cc_start: 0.9245 (t) cc_final: 0.9016 (m)
REVERT: A  345 SER cc_start: 0.9166 (t) cc_final: 0.8764 (p)
REVERT: A  476 SER cc_start: 0.8625 (t) cc_final: 0.8157 (p)
REVERT: A  537 TYR cc_start: 0.7992 (t80) cc_final: 0.7428 (t80)
REVERT: A  552 PHE cc_start: 0.8751 (m-10) cc_final: 0.8364 (m-80)
  outliers start: 30
  outliers final: 22
  residues processed: 108
  average time/residue: 0.0983
  time to fit residues: 14.5320
Evaluate side-chains
  114 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  363 CYS
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 161 HIS
A 413 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.101288 restraints weight = 6004.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.104775 restraints weight = 3152.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.107176 restraints weight = 2097.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3739  Z= 0.241
  Angle     :  0.738  15.441   5089  Z= 0.348
  Chirality :  0.043   0.364    603
  Planarity :  0.005   0.062    627
  Dihedral  :  5.434  59.294    508
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 28.24 %
    Favored  : 65.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.39), residues: 469
  helix:  1.97 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -1.05 (0.70), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 135 
 HIS   0.002   0.001   HIS A 296 
 PHE   0.008   0.001   PHE A 523 
 TYR   0.008   0.001   TYR A 547 
 ARG   0.003   0.000   ARG A 278 

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A  158 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8230 (p)
REVERT: A  305 VAL cc_start: 0.9200 (t) cc_final: 0.8904 (m)
REVERT: A  476 SER cc_start: 0.8605 (t) cc_final: 0.8136 (p)
REVERT: A  537 TYR cc_start: 0.8017 (t80) cc_final: 0.7462 (t80)
REVERT: A  552 PHE cc_start: 0.8765 (m-10) cc_final: 0.8416 (m-80)
  outliers start: 23
  outliers final: 21
  residues processed: 106
  average time/residue: 0.0964
  time to fit residues: 14.0008
Evaluate side-chains
  114 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  363 CYS
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  548 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0870
   chunk 34 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0270
   overall best weight:    0.3416

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.128883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.106102 restraints weight = 6003.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.109852 restraints weight = 3148.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.112388 restraints weight = 2073.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3739  Z= 0.188
  Angle     :  0.743  15.185   5089  Z= 0.342
  Chirality :  0.042   0.365    603
  Planarity :  0.004   0.055    627
  Dihedral  :  5.384  58.491    508
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 28.75 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.39), residues: 469
  helix:  2.04 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.11 (0.69), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 296 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.008   0.001   TYR A 547 
 ARG   0.003   0.000   ARG A 278 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1333.18 seconds
wall clock time: 24 minutes 45.47 seconds (1485.47 seconds total)