Starting phenix.real_space_refine
on Tue Mar  3 18:10:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mun_48638/03_2026/9mun_48638_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mun_48638/03_2026/9mun_48638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mun_48638/03_2026/9mun_48638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mun_48638/03_2026/9mun_48638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mun_48638/03_2026/9mun_48638_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mun_48638/03_2026/9mun_48638_trim.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.328
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2478      2.51       5
     N     572      2.21       5
     O     656      1.98       5
     H    3769      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7495
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 7455
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 25, 'TRANS': 445}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'GDS': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.09, per 1000 atoms: 0.15
  Number of scatterers: 7495
  At special positions: 0
  Unit cell: (81.2, 81.2, 87, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     O     656      8.00
     N     572      7.00
     C    2478      6.00
     H    3769      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 482 " - pdb=" SG  CYS A 499 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 490 " - pdb=" SG  CYS A 506 " distance=2.03

  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: 0.69
  Conformation dependent library (CDL) restraints added in 176.3 milliseconds
  

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  874

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 1 sheets defined
      83.7% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 102
      removed outlier: 3.531A  pdb=" N   SER A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 114 through 124
      Proline residue:  A 118  - end of helix
      removed outlier: 4.289A  pdb=" N   LYS A 122 " --> pdb=" O   PHE A 119 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   LEU A 123 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 132
    Processing helix  chain 'A' and resid 140 through 166
      Proline residue:  A 146  - end of helix
      removed outlier: 4.614A  pdb=" N   ASP A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   ARG A 164 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 172
      removed outlier: 3.831A  pdb=" N   ASP A 171 " --> pdb=" O   ASN A 168 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG A 172 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 168 through 172'
    Processing helix  chain 'A' and resid 175 through 205
    Processing helix  chain 'A' and resid 209 through 229
      removed outlier: 3.612A  pdb=" N   SER A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 237 through 244
    Processing helix  chain 'A' and resid 256 through 278
    Processing helix  chain 'A' and resid 294 through 307
    Processing helix  chain 'A' and resid 307 through 321
      removed outlier: 3.928A  pdb=" N   LYS A 321 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 339
      removed outlier: 3.818A  pdb=" N   THR A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   GLY A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   LEU A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 348
    Processing helix  chain 'A' and resid 351 through 359
      removed outlier: 3.913A  pdb=" N   LEU A 355 " --> pdb=" O   PRO A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 368
      removed outlier: 3.642A  pdb=" N   ALA A 368 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 396
      removed outlier: 4.324A  pdb=" N   PHE A 376 " --> pdb=" O   PRO A 372 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 411 through 443
      removed outlier: 3.611A  pdb=" N   ILE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 478
      Proline residue:  A 466  - end of helix
      removed outlier: 4.520A  pdb=" N   ASP A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      Proline residue:  A 476  - end of helix
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 511 through 531
      removed outlier: 3.590A  pdb=" N   VAL A 515 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 540
      removed outlier: 3.928A  pdb=" N   GLN A 539 " --> pdb=" O   PHE A 535 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ASP A 540 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 547
      removed outlier: 5.833A  pdb=" N   SER A 544 " --> pdb=" O   GLU A 541 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 479 through 482
      removed outlier: 3.706A  pdb=" N   LEU A 510 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   GLU A 481 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   THR A 508 " --> pdb=" O   GLU A 481 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    759 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        0.84 -     1.09: 3764
        1.09 -     1.34: 1107
        1.34 -     1.60: 2694
        1.60 -     1.85: 29
        1.85 -     2.10: 1
  Bond restraints: 7595
  Sorted by residual:
  bond pdb=" C5  GDS A 601 "
       pdb=" N4  GDS A 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.453 -0.120 2.00e-02 2.50e+03 3.60e+01
  bond pdb=" C2  GDS A 601 "
       pdb=" N3  GDS A 601 "
    ideal  model  delta    sigma   weight residual
    1.334  1.450 -0.116 2.00e-02 2.50e+03 3.36e+01
  bond pdb=" CD1 GDS A 601 "
       pdb=" N2  GDS A 601 "
    ideal  model  delta    sigma   weight residual
    1.339  1.455 -0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" CD6 GDS A 601 "
       pdb=" N5  GDS A 601 "
    ideal  model  delta    sigma   weight residual
    1.349  1.452 -0.103 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" CD1 GDS A 601 "
       pdb=" O1  GDS A 601 "
    ideal  model  delta    sigma   weight residual
    1.242  1.184  0.058 2.00e-02 2.50e+03 8.55e+00
  ... (remaining 7590 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 13641
        1.79 -     3.58: 102
        3.58 -     5.37: 22
        5.37 -     7.16: 6
        7.16 -     8.95: 4
  Bond angle restraints: 13775
  Sorted by residual:
  angle pdb=" C2  GDS A 601 "
        pdb=" CA2 GDS A 601 "
        pdb=" N2  GDS A 601 "
      ideal   model   delta    sigma   weight residual
     115.86  106.91    8.95 3.00e+00 1.11e-01 8.90e+00
  angle pdb=" CB1 GDS A 601 "
        pdb=" CG1 GDS A 601 "
        pdb=" CD1 GDS A 601 "
      ideal   model   delta    sigma   weight residual
     117.94  109.13    8.81 3.00e+00 1.11e-01 8.61e+00
  angle pdb=" OE5 GDS A 601 "
        pdb=" C4  GDS A 601 "
        pdb=" OE6 GDS A 601 "
      ideal   model   delta    sigma   weight residual
     127.28  119.92    7.36 3.00e+00 1.11e-01 6.01e+00
  angle pdb=" OE3 GDS A 601 "
        pdb=" C3  GDS A 601 "
        pdb=" OE4 GDS A 601 "
      ideal   model   delta    sigma   weight residual
     127.19  120.01    7.18 3.00e+00 1.11e-01 5.72e+00
  angle pdb=" CA5 GDS A 601 "
        pdb=" CB5 GDS A 601 "
        pdb=" SG5 GDS A 601 "
      ideal   model   delta    sigma   weight residual
     115.79  109.32    6.47 3.00e+00 1.11e-01 4.65e+00
  ... (remaining 13770 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.75: 3360
       25.75 -    51.50: 200
       51.50 -    77.24: 49
       77.24 -   102.99: 3
      102.99 -   128.74: 1
  Dihedral angle restraints: 3613
    sinusoidal: 1932
      harmonic: 1681
  Sorted by residual:
  dihedral pdb=" CB  CYS A 490 "
           pdb=" SG  CYS A 490 "
           pdb=" SG  CYS A 506 "
           pdb=" CB  CYS A 506 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.16  -80.16     1      1.00e+01 1.00e-02 7.96e+01
  dihedral pdb=" CB2 GDS A 601 "
           pdb=" C2  GDS A 601 "
           pdb=" CA2 GDS A 601 "
           pdb=" O2  GDS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      95.13  -33.61  128.74     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" CA  ASP A 175 "
           pdb=" CB  ASP A 175 "
           pdb=" CG  ASP A 175 "
           pdb=" OD1 ASP A 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.38   59.38     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 3610 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 566
       0.072 -    0.144: 44
       0.144 -    0.216: 1
       0.216 -    0.288: 0
       0.288 -    0.360: 1
  Chirality restraints: 612
  Sorted by residual:
  chirality pdb=" CA2 GDS A 601 "
            pdb=" CB2 GDS A 601 "
            pdb=" C2  GDS A 601 "
            pdb=" N2  GDS A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.24   -2.60    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CA1 GDS A 601 "
            pdb=" CB1 GDS A 601 "
            pdb=" C1  GDS A 601 "
            pdb=" N1  GDS A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.43   -2.61    0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CA  VAL A 340 "
            pdb=" N   VAL A 340 "
            pdb=" C   VAL A 340 "
            pdb=" CB  VAL A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.65e-01
  ... (remaining 609 not shown)

  Planarity restraints: 1081
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  95 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO A  96 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A  96 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  96 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 475 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.44e+00
        pdb=" N   PRO A 476 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 476 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 476 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 409 "   -0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO A 410 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 410 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 410 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1078 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 384
        2.19 -     2.80: 15450
        2.80 -     3.40: 21710
        3.40 -     4.00: 26697
        4.00 -     4.60: 41991
  Nonbonded interactions: 106232
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 372 "
            pdb=" HG  SER A 434 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" O   GLY A 449 "
            pdb=" HG1 THR A 453 "
     model   vdw
     1.643 2.450
  nonbonded pdb="HD22 ASN A 439 "
            pdb=" OD1 ASN A 456 "
     model   vdw
     1.645 2.450
  nonbonded pdb=" HH  TYR A 149 "
            pdb=" OG1 THR A 273 "
     model   vdw
     1.679 2.450
  nonbonded pdb=" O   ALA A 110 "
            pdb=" HG  SER A 113 "
     model   vdw
     1.690 2.450
  ... (remaining 106227 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.120
  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:             0.020
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.270
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
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      :  0.005   0.120   3828  Z= 0.239
  Angle     :  0.609   8.950   5225  Z= 0.284
  Chirality :  0.038   0.360    612
  Planarity :  0.004   0.040    637
  Dihedral  : 16.790 128.741   1364
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 15.46 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.39), residues: 467
  helix:  2.38 (0.28), residues: 341
  sheet:  None (None), residues: 0
  loop : -0.15 (0.55), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 207 
 TYR   0.014   0.001   TYR A 390 
 PHE   0.012   0.001   PHE A 183 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 3826)
  covalent geometry    : angle       0.60888 ( 5221)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.66167 (    4)
  hydrogen bonds       : bond        0.12559 (  260)
  hydrogen bonds       : angle       5.82397 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 LEU cc_start: 0.7687 (tt) cc_final: 0.7212 (mp)
REVERT: A  411 ILE cc_start: 0.8541 (tp) cc_final: 0.8076 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 80
  average time/residue: 0.1101
  time to fit residues: 11.3699
Evaluate side-chains
  80 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.159972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.127564 restraints weight = 12051.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.07
r_work: 0.3233 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.0526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3828  Z= 0.168
  Angle     :  0.511   5.059   5225  Z= 0.268
  Chirality :  0.037   0.135    612
  Planarity :  0.004   0.039    637
  Dihedral  : 11.099 127.942    544
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.97 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.38), residues: 467
  helix:  2.61 (0.26), residues: 347
  sheet:  None (None), residues: 0
  loop : -0.46 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.011   0.001   TYR A 390 
 PHE   0.014   0.001   PHE A 183 
 TRP   0.009   0.001   TRP A 465 
 HIS   0.001   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3826)
  covalent geometry    : angle       0.51061 ( 5221)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       0.70130 (    4)
  hydrogen bonds       : bond        0.04993 (  260)
  hydrogen bonds       : angle       4.40999 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  411 ILE cc_start: 0.8556 (tp) cc_final: 0.8114 (mp)
REVERT: A  436 MET cc_start: 0.8447 (mmm) cc_final: 0.8225 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 87
  average time/residue: 0.1093
  time to fit residues: 12.4093
Evaluate side-chains
  86 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.159790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.128043 restraints weight = 12045.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.06
r_work: 0.3235 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3828  Z= 0.137
  Angle     :  0.481   4.961   5225  Z= 0.249
  Chirality :  0.036   0.132    612
  Planarity :  0.004   0.038    637
  Dihedral  : 10.582 126.361    543
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.46 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.88 (0.39), residues: 467
  helix:  2.71 (0.27), residues: 346
  sheet:  None (None), residues: 0
  loop : -0.57 (0.55), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.017   0.001   PHE A 260 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.001   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3826)
  covalent geometry    : angle       0.48060 ( 5221)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.65124 (    4)
  hydrogen bonds       : bond        0.04524 (  260)
  hydrogen bonds       : angle       4.19416 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 SER cc_start: 0.8764 (m) cc_final: 0.8297 (p)
REVERT: A  175 ASP cc_start: 0.7733 (t70) cc_final: 0.7457 (t70)
REVERT: A  221 GLN cc_start: 0.8089 (tt0) cc_final: 0.7815 (tp40)
REVERT: A  395 TRP cc_start: 0.8266 (t-100) cc_final: 0.8009 (t60)
REVERT: A  411 ILE cc_start: 0.8571 (tp) cc_final: 0.8119 (mp)
REVERT: A  436 MET cc_start: 0.8461 (mmm) cc_final: 0.8228 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 85
  average time/residue: 0.1071
  time to fit residues: 11.9968
Evaluate side-chains
  85 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 221 GLN
A 464 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.156652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.124250 restraints weight = 12263.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.09
r_work: 0.3186 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3828  Z= 0.207
  Angle     :  0.513   4.980   5225  Z= 0.271
  Chirality :  0.038   0.135    612
  Planarity :  0.005   0.040    637
  Dihedral  : 10.543 124.894    543
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.97 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.38), residues: 467
  helix:  2.46 (0.26), residues: 346
  sheet:  None (None), residues: 0
  loop : -0.68 (0.56), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.016   0.001   TYR A 390 
 PHE   0.015   0.001   PHE A 183 
 TRP   0.011   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 3826)
  covalent geometry    : angle       0.51315 ( 5221)
  SS BOND              : bond        0.00376 (    2)
  SS BOND              : angle       0.75185 (    4)
  hydrogen bonds       : bond        0.04693 (  260)
  hydrogen bonds       : angle       4.24136 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 SER cc_start: 0.8860 (m) cc_final: 0.8402 (p)
REVERT: A  175 ASP cc_start: 0.7775 (t70) cc_final: 0.7321 (t70)
REVERT: A  362 ILE cc_start: 0.3555 (OUTLIER) cc_final: 0.3228 (mp)
REVERT: A  395 TRP cc_start: 0.8300 (t-100) cc_final: 0.8090 (t60)
REVERT: A  411 ILE cc_start: 0.8674 (tp) cc_final: 0.8252 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 90
  average time/residue: 0.1102
  time to fit residues: 13.0244
Evaluate side-chains
  90 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  522 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0770
   chunk 21 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   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 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.157398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.125074 restraints weight = 12197.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.09
r_work: 0.3200 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3828  Z= 0.172
  Angle     :  0.493   4.939   5225  Z= 0.258
  Chirality :  0.037   0.131    612
  Planarity :  0.005   0.040    637
  Dihedral  : 10.301 125.568    543
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.21 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.38), residues: 467
  helix:  2.44 (0.27), residues: 346
  sheet:  None (None), residues: 0
  loop : -0.69 (0.56), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.013   0.001   TYR A 390 
 PHE   0.012   0.001   PHE A 183 
 TRP   0.010   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3826)
  covalent geometry    : angle       0.49237 ( 5221)
  SS BOND              : bond        0.00281 (    2)
  SS BOND              : angle       0.70419 (    4)
  hydrogen bonds       : bond        0.04444 (  260)
  hydrogen bonds       : angle       4.16963 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 SER cc_start: 0.8799 (m) cc_final: 0.8329 (p)
REVERT: A  175 ASP cc_start: 0.7727 (t70) cc_final: 0.7211 (t70)
REVERT: A  362 ILE cc_start: 0.3489 (OUTLIER) cc_final: 0.3147 (mp)
REVERT: A  395 TRP cc_start: 0.8286 (t-100) cc_final: 0.8049 (t60)
REVERT: A  411 ILE cc_start: 0.8591 (tp) cc_final: 0.8144 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 90
  average time/residue: 0.0947
  time to fit residues: 11.4890
Evaluate side-chains
  91 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 TYR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  522 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0000
   chunk 13 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 464 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.157883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.125523 restraints weight = 12203.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.08
r_work: 0.3205 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3828  Z= 0.158
  Angle     :  0.485   4.915   5225  Z= 0.252
  Chirality :  0.036   0.133    612
  Planarity :  0.004   0.040    637
  Dihedral  : 10.100 126.430    543
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.21 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.38), residues: 467
  helix:  2.48 (0.27), residues: 347
  sheet:  None (None), residues: 0
  loop : -0.64 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.013   0.001   TYR A 390 
 PHE   0.013   0.001   PHE A 183 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3826)
  covalent geometry    : angle       0.48488 ( 5221)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       0.67929 (    4)
  hydrogen bonds       : bond        0.04307 (  260)
  hydrogen bonds       : angle       4.10473 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 SER cc_start: 0.8814 (m) cc_final: 0.8371 (p)
REVERT: A  175 ASP cc_start: 0.7742 (t70) cc_final: 0.7240 (t70)
REVERT: A  362 ILE cc_start: 0.3465 (OUTLIER) cc_final: 0.3125 (mp)
REVERT: A  395 TRP cc_start: 0.8325 (t-100) cc_final: 0.8058 (t60)
REVERT: A  399 LYS cc_start: 0.5473 (mmmt) cc_final: 0.5156 (mmmt)
REVERT: A  411 ILE cc_start: 0.8640 (tp) cc_final: 0.8218 (mp)
  outliers start: 9
  outliers final: 7
  residues processed: 90
  average time/residue: 0.0959
  time to fit residues: 11.5497
Evaluate side-chains
  93 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  149 TYR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  522 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0980
   chunk 29 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.158188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.126088 restraints weight = 12253.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.09
r_work: 0.3210 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3828  Z= 0.145
  Angle     :  0.484   4.883   5225  Z= 0.253
  Chirality :  0.037   0.148    612
  Planarity :  0.005   0.039    637
  Dihedral  : 10.033 126.907    543
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.21 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.38), residues: 467
  helix:  2.52 (0.27), residues: 348
  sheet:  None (None), residues: 0
  loop : -0.66 (0.56), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.011   0.001   TYR A 390 
 PHE   0.013   0.001   PHE A 183 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3826)
  covalent geometry    : angle       0.48370 ( 5221)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.66635 (    4)
  hydrogen bonds       : bond        0.04227 (  260)
  hydrogen bonds       : angle       4.06840 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 SER cc_start: 0.8820 (m) cc_final: 0.8370 (p)
REVERT: A  175 ASP cc_start: 0.7727 (t70) cc_final: 0.7203 (t70)
REVERT: A  362 ILE cc_start: 0.3450 (OUTLIER) cc_final: 0.3088 (mp)
REVERT: A  399 LYS cc_start: 0.5569 (mmmt) cc_final: 0.5213 (mmmt)
REVERT: A  411 ILE cc_start: 0.8623 (tp) cc_final: 0.8207 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1085
  time to fit residues: 12.6433
Evaluate side-chains
  90 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 TYR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  522 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.157488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.125277 restraints weight = 12174.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.08
r_work: 0.3199 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3828  Z= 0.170
  Angle     :  0.490   4.914   5225  Z= 0.256
  Chirality :  0.036   0.132    612
  Planarity :  0.005   0.040    637
  Dihedral  :  9.944 127.867    543
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.71 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.38), residues: 467
  helix:  2.44 (0.27), residues: 349
  sheet:  None (None), residues: 0
  loop : -0.65 (0.57), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 207 
 TYR   0.013   0.001   TYR A 390 
 PHE   0.013   0.001   PHE A 183 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.000   0.000   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3826)
  covalent geometry    : angle       0.49010 ( 5221)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       0.67366 (    4)
  hydrogen bonds       : bond        0.04290 (  260)
  hydrogen bonds       : angle       4.07925 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 SER cc_start: 0.8829 (m) cc_final: 0.8377 (p)
REVERT: A  175 ASP cc_start: 0.7733 (t70) cc_final: 0.7201 (t70)
REVERT: A  362 ILE cc_start: 0.3455 (OUTLIER) cc_final: 0.3095 (mp)
REVERT: A  399 LYS cc_start: 0.5645 (mmmt) cc_final: 0.5190 (mmmt)
REVERT: A  411 ILE cc_start: 0.8641 (tp) cc_final: 0.8217 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 90
  average time/residue: 0.0999
  time to fit residues: 12.0730
Evaluate side-chains
  90 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  522 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0870
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.158434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.126131 restraints weight = 12211.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.10
r_work: 0.3211 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3828  Z= 0.127
  Angle     :  0.474   4.857   5225  Z= 0.245
  Chirality :  0.036   0.133    612
  Planarity :  0.005   0.040    637
  Dihedral  :  9.781 128.257    543
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.71 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.39), residues: 467
  helix:  2.59 (0.27), residues: 349
  sheet:  None (None), residues: 0
  loop : -0.55 (0.58), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 172 
 TYR   0.011   0.001   TYR A 390 
 PHE   0.013   0.001   PHE A 183 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3826)
  covalent geometry    : angle       0.47368 ( 5221)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       0.67830 (    4)
  hydrogen bonds       : bond        0.04080 (  260)
  hydrogen bonds       : angle       4.00395 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 SER cc_start: 0.8764 (m) cc_final: 0.8323 (p)
REVERT: A  175 ASP cc_start: 0.7743 (t70) cc_final: 0.7183 (t70)
REVERT: A  362 ILE cc_start: 0.3413 (OUTLIER) cc_final: 0.3041 (mp)
REVERT: A  411 ILE cc_start: 0.8633 (tp) cc_final: 0.8212 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1030
  time to fit residues: 12.6262
Evaluate side-chains
  92 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 TYR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  522 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0870
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 1 optimal weight:    0.0970
   chunk 32 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.2554

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.159582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.127723 restraints weight = 12055.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.06
r_work: 0.3235 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3828  Z= 0.111
  Angle     :  0.466   4.987   5225  Z= 0.240
  Chirality :  0.035   0.135    612
  Planarity :  0.004   0.039    637
  Dihedral  :  9.657 128.715    543
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.21 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.93 (0.39), residues: 467
  helix:  2.71 (0.27), residues: 349
  sheet:  None (None), residues: 0
  loop : -0.51 (0.58), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 172 
 TYR   0.009   0.001   TYR A 390 
 PHE   0.013   0.001   PHE A 183 
 TRP   0.008   0.001   TRP A 465 
 HIS   0.001   0.000   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3826)
  covalent geometry    : angle       0.46621 ( 5221)
  SS BOND              : bond        0.00196 (    2)
  SS BOND              : angle       0.69451 (    4)
  hydrogen bonds       : bond        0.03921 (  260)
  hydrogen bonds       : angle       3.91858 (  759)

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

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

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  934 Ramachandran restraints generated.
    467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TYR cc_start: 0.8791 (m-80) cc_final: 0.8013 (m-80)
REVERT: A  120 SER cc_start: 0.8741 (m) cc_final: 0.8323 (p)
REVERT: A  175 ASP cc_start: 0.7728 (t70) cc_final: 0.7183 (t70)
REVERT: A  362 ILE cc_start: 0.3416 (OUTLIER) cc_final: 0.3013 (mp)
REVERT: A  399 LYS cc_start: 0.5462 (mmmt) cc_final: 0.5166 (mmmt)
REVERT: A  411 ILE cc_start: 0.8562 (tp) cc_final: 0.8192 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 90
  average time/residue: 0.0980
  time to fit residues: 11.7152
Evaluate side-chains
  92 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 TYR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  522 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    0.1980
   chunk 7 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   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 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.157593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.125720 restraints weight = 12232.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.06
r_work: 0.3209 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3828  Z= 0.148
  Angle     :  0.479   4.875   5225  Z= 0.249
  Chirality :  0.036   0.134    612
  Planarity :  0.005   0.040    637
  Dihedral  :  9.641 128.880    543
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.21 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.39), residues: 467
  helix:  2.60 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.48 (0.61), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 207 
 TYR   0.012   0.001   TYR A 390 
 PHE   0.013   0.001   PHE A 183 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3826)
  covalent geometry    : angle       0.47918 ( 5221)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       0.68864 (    4)
  hydrogen bonds       : bond        0.04084 (  260)
  hydrogen bonds       : angle       3.95639 (  759)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2327.63 seconds
wall clock time: 40 minutes 0.51 seconds (2400.51 seconds total)