Starting phenix.real_space_refine
on Mon Feb 10 23:47:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jts_36651/02_2025/8jts_36651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jts_36651/02_2025/8jts_36651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jts_36651/02_2025/8jts_36651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jts_36651/02_2025/8jts_36651.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jts_36651/02_2025/8jts_36651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jts_36651/02_2025/8jts_36651.cif"
  }
  resolution = 4.14
  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=   0.002 sd=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2190      2.51       5
     N     534      2.21       5
     O     583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3330
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3321
          Classifications: {'peptide': 461}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 20, 'TRANS': 440}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 280
          Unresolved non-hydrogen angles: 342
          Unresolved non-hydrogen dihedrals: 239
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 157
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'MF8': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.45, per 1000 atoms: 0.74
  Number of scatterers: 3330
  At special positions: 0
  Unit cell: (94.1775, 58.455, 67.115, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O     583      8.00
     N     534      7.00
     C    2190      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 413.1 milliseconds
  

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  850

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 0 sheets defined
      77.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
    Processing helix  chain 'A' and resid 15 through 30
    Processing helix  chain 'A' and resid 32 through 37
      removed outlier: 3.670A  pdb=" N   CYS A  36 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 146 through 166
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 174 through 195
    Processing helix  chain 'A' and resid 199 through 228
    Processing helix  chain 'A' and resid 232 through 258
    Processing helix  chain 'A' and resid 260 through 279
      removed outlier: 3.668A  pdb=" N   LEU A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      Proline residue:  A 271  - end of helix
      removed outlier: 3.896A  pdb=" N   TYR A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 315 through 320
    Processing helix  chain 'A' and resid 340 through 368
    Processing helix  chain 'A' and resid 376 through 397
      removed outlier: 3.657A  pdb=" N   VAL A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ILE A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      Proline residue:  A 388  - end of helix
    Processing helix  chain 'A' and resid 403 through 423
      removed outlier: 3.865A  pdb=" N   MET A 420 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   ILE A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 456
      removed outlier: 4.146A  pdb=" N   ILE A 446 " --> pdb=" O   ILE A 442 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 463
      removed outlier: 4.081A  pdb=" N   ASN A 463 " --> pdb=" O   THR A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 3.855A  pdb=" N   CYS A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 491
      Proline residue:  A 481  - end of helix
      removed outlier: 3.888A  pdb=" N   GLU A 489 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 510
      removed outlier: 3.676A  pdb=" N   ILE A 497 " --> pdb=" O   ALA A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 531
      removed outlier: 3.986A  pdb=" N   LEU A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)

    238 hydrogen bonds defined for protein.
    714 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: 0.92

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 533
        1.30 -     1.43: 891
        1.43 -     1.56: 1950
        1.56 -     1.69: 0
        1.69 -     1.82: 35
  Bond restraints: 3409
  Sorted by residual:
  bond pdb=" CA  THR A 356 "
       pdb=" C   THR A 356 "
    ideal  model  delta    sigma   weight residual
    1.524  1.414  0.110 1.27e-02 6.20e+03 7.52e+01
  bond pdb=" C07 MF8 A 601 "
       pdb=" N08 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.281  1.447 -0.166 2.00e-02 2.50e+03 6.89e+01
  bond pdb=" N   ARG A 439 "
       pdb=" CA  ARG A 439 "
    ideal  model  delta    sigma   weight residual
    1.459  1.363  0.095 1.24e-02 6.50e+03 5.90e+01
  bond pdb=" C07 MF8 A 601 "
       pdb=" N06 MF8 A 601 "
    ideal  model  delta    sigma   weight residual
    1.393  1.245  0.148 2.00e-02 2.50e+03 5.47e+01
  bond pdb=" CA  ASP A 357 "
       pdb=" CB  ASP A 357 "
    ideal  model  delta    sigma   weight residual
    1.530  1.432  0.098 1.57e-02 4.06e+03 3.91e+01
  ... (remaining 3404 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 4485
        1.96 -     3.91: 134
        3.91 -     5.87: 39
        5.87 -     7.82: 12
        7.82 -     9.78: 6
  Bond angle restraints: 4676
  Sorted by residual:
  angle pdb=" N   THR A 356 "
        pdb=" CA  THR A 356 "
        pdb=" C   THR A 356 "
      ideal   model   delta    sigma   weight residual
     111.07  102.52    8.55 1.07e+00 8.73e-01 6.38e+01
  angle pdb=" C   THR A 356 "
        pdb=" N   ASP A 357 "
        pdb=" CA  ASP A 357 "
      ideal   model   delta    sigma   weight residual
     120.65  110.87    9.78 1.32e+00 5.74e-01 5.49e+01
  angle pdb=" CA  ASP A 357 "
        pdb=" C   ASP A 357 "
        pdb=" N   SER A 358 "
      ideal   model   delta    sigma   weight residual
     116.92  124.94   -8.02 1.16e+00 7.43e-01 4.79e+01
  angle pdb=" N   GLN A 362 "
        pdb=" CA  GLN A 362 "
        pdb=" C   GLN A 362 "
      ideal   model   delta    sigma   weight residual
     111.75  104.24    7.51 1.28e+00 6.10e-01 3.44e+01
  angle pdb=" O   ASP A 357 "
        pdb=" C   ASP A 357 "
        pdb=" N   SER A 358 "
      ideal   model   delta    sigma   weight residual
     122.03  116.89    5.14 1.04e+00 9.25e-01 2.44e+01
  ... (remaining 4671 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 1767
       17.47 -    34.94: 148
       34.94 -    52.41: 29
       52.41 -    69.89: 7
       69.89 -    87.36: 3
  Dihedral angle restraints: 1954
    sinusoidal: 634
      harmonic: 1320
  Sorted by residual:
  dihedral pdb=" CA  ILE A 442 "
           pdb=" C   ILE A 442 "
           pdb=" N   THR A 443 "
           pdb=" CA  THR A 443 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.77   28.23     0      5.00e+00 4.00e-02 3.19e+01
  dihedral pdb=" CA  THR A 356 "
           pdb=" C   THR A 356 "
           pdb=" N   ASP A 357 "
           pdb=" CA  ASP A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.75  -21.25     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  MET A 448 "
           pdb=" C   MET A 448 "
           pdb=" N   ILE A 449 "
           pdb=" CA  ILE A 449 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.03  -18.97     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 1951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 465
       0.056 -    0.112: 92
       0.112 -    0.168: 8
       0.168 -    0.224: 2
       0.224 -    0.280: 4
  Chirality restraints: 571
  Sorted by residual:
  chirality pdb=" CG  LEU A  25 "
            pdb=" CB  LEU A  25 "
            pdb=" CD1 LEU A  25 "
            pdb=" CD2 LEU A  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  ASP A 357 "
            pdb=" N   ASP A 357 "
            pdb=" C   ASP A 357 "
            pdb=" CB  ASP A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  TYR A 361 "
            pdb=" N   TYR A 361 "
            pdb=" C   TYR A 361 "
            pdb=" CB  TYR A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 568 not shown)

  Planarity restraints: 582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C01 MF8 A 601 "   -0.070 2.00e-02 2.50e+03   4.80e-01 5.19e+03
        pdb=" C03 MF8 A 601 "    0.458 2.00e-02 2.50e+03
        pdb=" C04 MF8 A 601 "   -0.216 2.00e-02 2.50e+03
        pdb=" C07 MF8 A 601 "    0.227 2.00e-02 2.50e+03
        pdb=" N02 MF8 A 601 "    0.055 2.00e-02 2.50e+03
        pdb=" N05 MF8 A 601 "   -1.078 2.00e-02 2.50e+03
        pdb=" N06 MF8 A 601 "    0.514 2.00e-02 2.50e+03
        pdb=" N08 MF8 A 601 "   -0.349 2.00e-02 2.50e+03
        pdb=" N09 MF8 A 601 "    0.459 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 270 "   -0.044 5.00e-02 4.00e+02   6.57e-02 6.90e+00
        pdb=" N   PRO A 271 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 361 "   -0.012 2.00e-02 2.50e+03   2.37e-02 5.63e+00
        pdb=" C   TYR A 361 "    0.041 2.00e-02 2.50e+03
        pdb=" O   TYR A 361 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN A 362 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 579 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 738
        2.78 -     3.31: 3476
        3.31 -     3.84: 5593
        3.84 -     4.37: 5722
        4.37 -     4.90: 9809
  Nonbonded interactions: 25338
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 167 "
            pdb=" ND2 ASN A 463 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG  SER A 424 "
            pdb=" OD1 ASP A 426 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   GLY A  12 "
            pdb=" NE2 GLN A  18 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" OD1 ASN A 198 "
            pdb=" OG  SER A 201 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   VAL A 141 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.367 3.040
  ... (remaining 25333 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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.470
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6651
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   0.166   3409  Z= 0.445
  Angle     :  0.933   9.780   4676  Z= 0.539
  Chirality :  0.049   0.280    571
  Planarity :  0.021   0.480    582
  Dihedral  : 14.111  87.356   1104
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.94 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.39), residues: 457
  helix:  0.25 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.17 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 354 
 HIS   0.001   0.000   HIS A 260 
 PHE   0.021   0.002   PHE A 151 
 TYR   0.010   0.001   TYR A 256 
 ARG   0.006   0.001   ARG A 439 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6584 (mm-30)
REVERT: A  293 LYS cc_start: 0.8310 (mttm) cc_final: 0.8109 (mttm)
REVERT: A  352 TYR cc_start: 0.5406 (m-80) cc_final: 0.5079 (m-80)
REVERT: A  361 TYR cc_start: 0.8688 (t80) cc_final: 0.8330 (t80)
REVERT: A  449 ILE cc_start: 0.8890 (tt) cc_final: 0.8569 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 94
  average time/residue: 0.1161
  time to fit residues: 14.1176
Evaluate side-chains
  80 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.0020
   chunk 34 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.218318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.191749 restraints weight = 4723.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.196843 restraints weight = 2624.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.200349 restraints weight = 1684.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.1031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3409  Z= 0.182
  Angle     :  0.596   6.904   4676  Z= 0.298
  Chirality :  0.039   0.158    571
  Planarity :  0.005   0.062    582
  Dihedral  :  4.395  19.039    479
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.32 (0.39), residues: 457
  helix:  0.78 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.12 (0.58), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 217 
 HIS   0.001   0.000   HIS A 260 
 PHE   0.019   0.001   PHE A  41 
 TYR   0.010   0.001   TYR A 256 
 ARG   0.002   0.000   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6610 (mm-30)
REVERT: A  352 TYR cc_start: 0.5487 (m-80) cc_final: 0.5260 (m-80)
REVERT: A  449 ILE cc_start: 0.8866 (tt) cc_final: 0.8519 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1162
  time to fit residues: 14.1053
Evaluate side-chains
  80 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 6 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS
A 463 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.216285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.190286 restraints weight = 4636.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.195288 restraints weight = 2564.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.198685 restraints weight = 1648.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3409  Z= 0.182
  Angle     :  0.615   7.143   4676  Z= 0.302
  Chirality :  0.039   0.157    571
  Planarity :  0.005   0.061    582
  Dihedral  :  4.247  16.477    479
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.67 (0.40), residues: 457
  helix:  1.05 (0.29), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.09 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 261 
 HIS   0.000   0.000   HIS A 260 
 PHE   0.016   0.001   PHE A  41 
 TYR   0.015   0.001   TYR A 361 
 ARG   0.003   0.000   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6643 (mm-30)
REVERT: A  449 ILE cc_start: 0.8807 (tt) cc_final: 0.8553 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1118
  time to fit residues: 13.8257
Evaluate side-chains
  85 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 14 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   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 186 ASN
A 463 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.210058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.187082 restraints weight = 4702.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.191401 restraints weight = 2608.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.194235 restraints weight = 1677.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3409  Z= 0.179
  Angle     :  0.608   7.197   4676  Z= 0.301
  Chirality :  0.040   0.182    571
  Planarity :  0.005   0.061    582
  Dihedral  :  4.177  15.639    479
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.69 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.40), residues: 457
  helix:  1.15 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.14 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.022   0.002   PHE A 151 
 TYR   0.011   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6461 (mm-30)
REVERT: A  287 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8317 (ttm-80)
REVERT: A  426 ASP cc_start: 0.7987 (p0) cc_final: 0.7426 (m-30)
REVERT: A  449 ILE cc_start: 0.8788 (tt) cc_final: 0.8534 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1169
  time to fit residues: 14.9358
Evaluate side-chains
  82 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0970
   chunk 1 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0670
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.216469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.190566 restraints weight = 4708.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.195391 restraints weight = 2626.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.198731 restraints weight = 1702.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3409  Z= 0.166
  Angle     :  0.605   7.007   4676  Z= 0.297
  Chirality :  0.039   0.162    571
  Planarity :  0.005   0.059    582
  Dihedral  :  4.141  15.282    479
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.92 (0.40), residues: 457
  helix:  1.28 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.14 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 217 
 HIS   0.001   0.000   HIS A 367 
 PHE   0.019   0.001   PHE A  41 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.003   0.000   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6404 (mm-30)
REVERT: A  287 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8308 (ttm-80)
REVERT: A  426 ASP cc_start: 0.8369 (p0) cc_final: 0.7878 (m-30)
REVERT: A  449 ILE cc_start: 0.8819 (tt) cc_final: 0.8546 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1120
  time to fit residues: 13.5228
Evaluate side-chains
  82 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0870
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0570
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.216263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.189899 restraints weight = 4826.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.194871 restraints weight = 2628.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.198386 restraints weight = 1678.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3409  Z= 0.170
  Angle     :  0.621   7.203   4676  Z= 0.303
  Chirality :  0.039   0.155    571
  Planarity :  0.005   0.057    582
  Dihedral  :  4.077  14.826    479
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  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:  0.94 (0.40), residues: 457
  helix:  1.29 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.12 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 217 
 HIS   0.000   0.000   HIS A 260 
 PHE   0.021   0.001   PHE A 151 
 TYR   0.010   0.001   TYR A 361 
 ARG   0.003   0.000   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6315 (mm-30)
REVERT: A  287 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8325 (ttm-80)
REVERT: A  426 ASP cc_start: 0.8438 (p0) cc_final: 0.7924 (m-30)
REVERT: A  449 ILE cc_start: 0.8832 (tt) cc_final: 0.8528 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1134
  time to fit residues: 13.6852
Evaluate side-chains
  86 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
A 463 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.209760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.183896 restraints weight = 4748.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.188592 restraints weight = 2638.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.191476 restraints weight = 1719.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3409  Z= 0.208
  Angle     :  0.650   6.574   4676  Z= 0.329
  Chirality :  0.042   0.242    571
  Planarity :  0.005   0.058    582
  Dihedral  :  4.267  15.870    479
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  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:  0.87 (0.40), residues: 457
  helix:  1.21 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.10 (0.60), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A 304 
 PHE   0.021   0.002   PHE A  41 
 TYR   0.014   0.001   TYR A 256 
 ARG   0.003   0.001   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.6397 (mm-30) cc_final: 0.6187 (mm-30)
REVERT: A  426 ASP cc_start: 0.8511 (p0) cc_final: 0.8013 (m-30)
REVERT: A  449 ILE cc_start: 0.8877 (tt) cc_final: 0.8598 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1107
  time to fit residues: 13.8330
Evaluate side-chains
  84 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.213173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.187270 restraints weight = 4723.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.192289 restraints weight = 2610.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.195759 restraints weight = 1674.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3409  Z= 0.182
  Angle     :  0.652   7.977   4676  Z= 0.322
  Chirality :  0.041   0.201    571
  Planarity :  0.005   0.059    582
  Dihedral  :  4.170  15.837    479
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.40), residues: 457
  helix:  1.25 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.10 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 217 
 HIS   0.000   0.000   HIS A 260 
 PHE   0.023   0.002   PHE A 151 
 TYR   0.010   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6501 (mm-30)
REVERT: A  287 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8388 (ttm-80)
REVERT: A  426 ASP cc_start: 0.8430 (p0) cc_final: 0.7933 (m-30)
REVERT: A  449 ILE cc_start: 0.8867 (tt) cc_final: 0.8634 (tt)
REVERT: A  478 ILE cc_start: 0.8882 (mt) cc_final: 0.8676 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1132
  time to fit residues: 14.3959
Evaluate side-chains
  84 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.211075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.184269 restraints weight = 4696.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.189344 restraints weight = 2596.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.192389 restraints weight = 1675.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3409  Z= 0.211
  Angle     :  0.660   7.737   4676  Z= 0.333
  Chirality :  0.042   0.214    571
  Planarity :  0.005   0.059    582
  Dihedral  :  4.270  16.935    479
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.40), residues: 457
  helix:  1.22 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.08 (0.60), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 288 
 HIS   0.000   0.000   HIS A 304 
 PHE   0.025   0.002   PHE A  41 
 TYR   0.012   0.001   TYR A 256 
 ARG   0.001   0.000   ARG A 402 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  287 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8360 (ttm-80)
REVERT: A  352 TYR cc_start: 0.5693 (m-80) cc_final: 0.5375 (m-80)
REVERT: A  426 ASP cc_start: 0.8443 (p0) cc_final: 0.7963 (m-30)
REVERT: A  449 ILE cc_start: 0.8968 (tt) cc_final: 0.8668 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1214
  time to fit residues: 15.0563
Evaluate side-chains
  84 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0270
   chunk 24 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.212408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.186189 restraints weight = 4733.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.191264 restraints weight = 2575.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.194344 restraints weight = 1640.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3409  Z= 0.189
  Angle     :  0.659   7.970   4676  Z= 0.328
  Chirality :  0.041   0.203    571
  Planarity :  0.005   0.056    582
  Dihedral  :  4.268  17.197    479
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.02 (0.40), residues: 457
  helix:  1.32 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.01 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 288 
 HIS   0.000   0.000   HIS A 260 
 PHE   0.023   0.001   PHE A 151 
 TYR   0.010   0.001   TYR A 256 
 ARG   0.005   0.000   ARG A 175 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  287 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8326 (ttm-80)
REVERT: A  426 ASP cc_start: 0.8420 (p0) cc_final: 0.7945 (m-30)
REVERT: A  449 ILE cc_start: 0.8938 (tt) cc_final: 0.8623 (tt)
REVERT: A  478 ILE cc_start: 0.8871 (mt) cc_final: 0.8663 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1017
  time to fit residues: 12.8377
Evaluate side-chains
  87 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 10 optimal weight:    0.0870
   chunk 41 optimal weight:    0.0010
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.5766

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.213213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.186469 restraints weight = 4694.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.191562 restraints weight = 2568.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.194717 restraints weight = 1639.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3409  Z= 0.197
  Angle     :  0.661   7.773   4676  Z= 0.328
  Chirality :  0.041   0.209    571
  Planarity :  0.005   0.057    582
  Dihedral  :  4.193  17.028    479
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  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:  1.10 (0.40), residues: 457
  helix:  1.38 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -0.98 (0.60), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 217 
 HIS   0.001   0.000   HIS A 260 
 PHE   0.019   0.001   PHE A  41 
 TYR   0.010   0.001   TYR A 256 
 ARG   0.004   0.000   ARG A 175 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1296.67 seconds
wall clock time: 23 minutes 44.32 seconds (1424.32 seconds total)