Starting phenix.real_space_refine
on Sat Apr 26 23:57:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzs_41768/04_2025/8tzs_41768.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzs_41768/04_2025/8tzs_41768.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzs_41768/04_2025/8tzs_41768.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzs_41768/04_2025/8tzs_41768.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzs_41768/04_2025/8tzs_41768.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzs_41768/04_2025/8tzs_41768.cif"
  }
  resolution = 3.84
  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=  -0.000 sd=   0.012
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      36      5.16       5
     C    2594      2.51       5
     N     637      2.21       5
     O     647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3914
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3914
          Classifications: {'peptide': 480}
          Link IDs: {'PTRANS': 20, 'TRANS': 459}
          Chain breaks: 2
  Time building chain proxies: 2.93, per 1000 atoms: 0.75
  Number of scatterers: 3914
  At special positions: 0
  Unit cell: (86.346, 103.32, 78.228, 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      36     16.00
     O     647      8.00
     N     637      7.00
     C    2594      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 179 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 863.0 milliseconds
  

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  902

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 2 sheets defined
      54.4% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
    Processing helix  chain 'A' and resid 10 through 36
      removed outlier: 3.868A  pdb=" N   ILE A  16 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL A  17 " --> pdb=" O   LYS A  13 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLY A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLY A  33 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
      removed outlier: 4.043A  pdb=" N   GLN A 125 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 173
    Processing helix  chain 'A' and resid 227 through 258
      removed outlier: 3.588A  pdb=" N   LYS A 232 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      Proline residue:  A 243  - end of helix
    Processing helix  chain 'A' and resid 264 through 282
      removed outlier: 3.630A  pdb=" N   PHE A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 286 through 291
      removed outlier: 4.112A  pdb=" N   GLY A 290 " --> pdb=" O   TRP A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 322
      removed outlier: 3.708A  pdb=" N   ASP A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ILE A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 334
    Processing helix  chain 'A' and resid 335 through 360
      Proline residue:  A 341  - end of helix
      removed outlier: 3.753A  pdb=" N   VAL A 344 " --> pdb=" O   GLY A 340 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   PHE A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 351 " --> pdb=" O   PHE A 347 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   PHE A 352 " --> pdb=" O   CYS A 348 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   ASP A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 413
      removed outlier: 3.611A  pdb=" N   SER A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   GLY A 409 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LYS A 410 " --> pdb=" O   ASN A 406 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 456
    Processing helix  chain 'A' and resid 473 through 493
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 46
      removed outlier: 5.976A  pdb=" N   ILE A 216 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ALA A 119 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   MET A 110 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLU A 186 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   PHE A 112 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.991A  pdb=" N   MET A 134 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   ARG A 155 " --> pdb=" O   MET A 134 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL A 136 " --> pdb=" O   HIS A 153 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   HIS A 153 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU A 138 " --> pdb=" O   MET A 151 " (cutoff:3.500A)

    219 hydrogen bonds defined for protein.
    633 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: 0.99

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1185
        1.35 -     1.46: 1036
        1.46 -     1.58: 1747
        1.58 -     1.70: 2
        1.70 -     1.81: 60
  Bond restraints: 4030
  Sorted by residual:
  bond pdb=" CB  PRO A 263 "
       pdb=" CG  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.492  1.667 -0.175 5.00e-02 4.00e+02 1.22e+01
  bond pdb=" CG  PRO A 263 "
       pdb=" CD  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.503  1.390  0.113 3.40e-02 8.65e+02 1.10e+01
  bond pdb=" N   PRO A 263 "
       pdb=" CD  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.473  1.514 -0.041 1.40e-02 5.10e+03 8.64e+00
  bond pdb=" N   PRO A 263 "
       pdb=" CA  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.465  1.444  0.020 1.11e-02 8.12e+03 3.36e+00
  bond pdb=" CB  PRO A 170 "
       pdb=" CG  PRO A 170 "
    ideal  model  delta    sigma   weight residual
    1.492  1.580 -0.088 5.00e-02 4.00e+02 3.08e+00
  ... (remaining 4025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 5404
        3.21 -     6.41: 40
        6.41 -     9.62: 7
        9.62 -    12.82: 4
       12.82 -    16.03: 2
  Bond angle restraints: 5457
  Sorted by residual:
  angle pdb=" CA  PRO A 263 "
        pdb=" N   PRO A 263 "
        pdb=" CD  PRO A 263 "
      ideal   model   delta    sigma   weight residual
     112.00   95.97   16.03 1.40e+00 5.10e-01 1.31e+02
  angle pdb=" N   PRO A 263 "
        pdb=" CD  PRO A 263 "
        pdb=" CG  PRO A 263 "
      ideal   model   delta    sigma   weight residual
     103.20   93.36    9.84 1.50e+00 4.44e-01 4.30e+01
  angle pdb=" CA  PRO A 170 "
        pdb=" N   PRO A 170 "
        pdb=" CD  PRO A 170 "
      ideal   model   delta    sigma   weight residual
     112.00  105.41    6.59 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" CA  LEU A 440 "
        pdb=" CB  LEU A 440 "
        pdb=" CG  LEU A 440 "
      ideal   model   delta    sigma   weight residual
     116.30  131.82  -15.52 3.50e+00 8.16e-02 1.97e+01
  angle pdb=" CA  CYS A 179 "
        pdb=" CB  CYS A 179 "
        pdb=" SG  CYS A 179 "
      ideal   model   delta    sigma   weight residual
     114.40  124.10   -9.70 2.30e+00 1.89e-01 1.78e+01
  ... (remaining 5452 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 2018
       16.01 -    32.02: 233
       32.02 -    48.04: 78
       48.04 -    64.05: 10
       64.05 -    80.06: 5
  Dihedral angle restraints: 2344
    sinusoidal: 951
      harmonic: 1393
  Sorted by residual:
  dihedral pdb=" CA  CYS A 179 "
           pdb=" C   CYS A 179 "
           pdb=" N   ASP A 180 "
           pdb=" CA  ASP A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.97  -48.03     0      5.00e+00 4.00e-02 9.23e+01
  dihedral pdb=" CA  LYS A 161 "
           pdb=" C   LYS A 161 "
           pdb=" N   CYS A 162 "
           pdb=" CA  CYS A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.29  -31.71     0      5.00e+00 4.00e-02 4.02e+01
  dihedral pdb=" CA  GLU A 178 "
           pdb=" C   GLU A 178 "
           pdb=" N   CYS A 179 "
           pdb=" CA  CYS A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.47  -22.53     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 2341 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 457
       0.053 -    0.106: 128
       0.106 -    0.158: 8
       0.158 -    0.211: 1
       0.211 -    0.264: 3
  Chirality restraints: 597
  Sorted by residual:
  chirality pdb=" CB  ILE A 216 "
            pdb=" CA  ILE A 216 "
            pdb=" CG1 ILE A 216 "
            pdb=" CG2 ILE A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  CYS A 179 "
            pdb=" N   CYS A 179 "
            pdb=" C   CYS A 179 "
            pdb=" CB  CYS A 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  PRO A 263 "
            pdb=" N   PRO A 263 "
            pdb=" C   PRO A 263 "
            pdb=" CB  PRO A 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 594 not shown)

  Planarity restraints: 672
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 169 "    0.070 5.00e-02 4.00e+02   1.03e-01 1.68e+01
        pdb=" N   PRO A 170 "   -0.177 5.00e-02 4.00e+02
        pdb=" CA  PRO A 170 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 170 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 262 "   -0.068 5.00e-02 4.00e+02   9.20e-02 1.35e+01
        pdb=" N   PRO A 263 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 263 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 263 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 490 "    0.010 2.00e-02 2.50e+03   1.10e-02 2.12e+00
        pdb=" CG  PHE A 490 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 490 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 490 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 490 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 490 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 490 "    0.001 2.00e-02 2.50e+03
  ... (remaining 669 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 155
        2.72 -     3.26: 4179
        3.26 -     3.81: 6425
        3.81 -     4.35: 7251
        4.35 -     4.90: 12405
  Nonbonded interactions: 30415
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A   8 "
            pdb=" OG  SER A 495 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" NH1 ARG A 158 "
            pdb=" O   PRO A 183 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O   MET A   9 "
            pdb=" NH2 ARG A 431 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" O   THR A 371 "
            pdb=" N   GLY A 374 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   GLN A 326 "
            pdb=" NH1 ARG A 329 "
     model   vdw
     2.289 3.120
  ... (remaining 30410 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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.610
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
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   0.175   4032  Z= 0.206
  Angle     :  0.882  16.031   5461  Z= 0.482
  Chirality :  0.047   0.264    597
  Planarity :  0.007   0.103    672
  Dihedral  : 15.830  80.062   1436
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 20.57 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

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:  0.65 (0.38), residues: 474
  helix:  1.37 (0.32), residues: 223
  sheet:  0.18 (0.61), residues: 67
  loop : -0.56 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 192 
 PHE   0.026   0.002   PHE A 490 
 TYR   0.016   0.002   TYR A  45 
 ARG   0.002   0.000   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14113 (  219)
  hydrogen bonds       : angle       6.31322 (  633)
  SS BOND              : bond        0.00476 (    2)
  SS BOND              : angle       5.13274 (    4)
  covalent geometry    : bond        0.00531 ( 4030)
  covalent geometry    : angle       0.87118 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7109 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1239
  time to fit residues: 15.7196
Evaluate side-chains
  92 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.0770
   chunk 36 optimal weight:    0.3980
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8142

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.156791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.126740 restraints weight = 8311.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.130302 restraints weight = 4789.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132815 restraints weight = 3362.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4032  Z= 0.144
  Angle     :  0.651  10.594   5461  Z= 0.338
  Chirality :  0.045   0.256    597
  Planarity :  0.005   0.060    672
  Dihedral  :  5.384  40.040    511
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.97 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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:  0.96 (0.38), residues: 474
  helix:  1.55 (0.32), residues: 229
  sheet:  0.46 (0.61), residues: 67
  loop : -0.44 (0.50), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 192 
 PHE   0.016   0.002   PHE A 318 
 TYR   0.012   0.002   TYR A  45 
 ARG   0.002   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04700 (  219)
  hydrogen bonds       : angle       4.74840 (  633)
  SS BOND              : bond        0.00738 (    2)
  SS BOND              : angle       1.78302 (    4)
  covalent geometry    : bond        0.00337 ( 4030)
  covalent geometry    : angle       0.64915 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 TYR cc_start: 0.8009 (t80) cc_final: 0.7679 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 111
  average time/residue: 0.1289
  time to fit residues: 18.5559
Evaluate side-chains
  107 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  439 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0050
   chunk 27 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.7194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.157117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.128271 restraints weight = 8366.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.131573 restraints weight = 5002.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133918 restraints weight = 3579.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4032  Z= 0.132
  Angle     :  0.619  12.831   5461  Z= 0.316
  Chirality :  0.043   0.198    597
  Planarity :  0.004   0.046    672
  Dihedral  :  5.052  37.078    511
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 18.91 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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:  1.24 (0.39), residues: 474
  helix:  1.82 (0.33), residues: 229
  sheet:  0.60 (0.58), residues: 67
  loop : -0.35 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 192 
 PHE   0.016   0.002   PHE A 490 
 TYR   0.016   0.001   TYR A  45 
 ARG   0.002   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  219)
  hydrogen bonds       : angle       4.34071 (  633)
  SS BOND              : bond        0.00481 (    2)
  SS BOND              : angle       1.72622 (    4)
  covalent geometry    : bond        0.00300 ( 4030)
  covalent geometry    : angle       0.61739 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 TYR cc_start: 0.8100 (t80) cc_final: 0.7847 (t80)
REVERT: A  489 MET cc_start: 0.8718 (mtm) cc_final: 0.8516 (mtm)
  outliers start: 18
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1281
  time to fit residues: 18.1890
Evaluate side-chains
  111 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0570
   chunk 17 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9702

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
A 331 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.156099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.127343 restraints weight = 8191.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.130750 restraints weight = 4899.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133104 restraints weight = 3471.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4032  Z= 0.140
  Angle     :  0.625  12.002   5461  Z= 0.315
  Chirality :  0.043   0.153    597
  Planarity :  0.004   0.037    672
  Dihedral  :  4.919  32.821    511
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 19.15 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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:  1.35 (0.39), residues: 474
  helix:  1.98 (0.33), residues: 228
  sheet:  0.69 (0.57), residues: 67
  loop : -0.42 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.020   0.002   PHE A 490 
 TYR   0.011   0.001   TYR A  45 
 ARG   0.003   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04154 (  219)
  hydrogen bonds       : angle       4.12669 (  633)
  SS BOND              : bond        0.00509 (    2)
  SS BOND              : angle       1.20484 (    4)
  covalent geometry    : bond        0.00324 ( 4030)
  covalent geometry    : angle       0.62443 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8551 (pt)
REVERT: A  432 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.5942 (t80)
REVERT: A  478 TYR cc_start: 0.8083 (t80) cc_final: 0.7843 (t80)
  outliers start: 26
  outliers final: 19
  residues processed: 112
  average time/residue: 0.1294
  time to fit residues: 18.8626
Evaluate side-chains
  113 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   chunk 35 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.156848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.128069 restraints weight = 8438.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.131493 restraints weight = 5001.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133860 restraints weight = 3536.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4032  Z= 0.130
  Angle     :  0.637  14.196   5461  Z= 0.314
  Chirality :  0.042   0.132    597
  Planarity :  0.004   0.033    672
  Dihedral  :  4.806  29.595    511
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 20.09 %
    Favored  : 73.76 %
  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:  1.51 (0.39), residues: 474
  helix:  1.98 (0.33), residues: 230
  sheet:  0.81 (0.58), residues: 74
  loop : -0.22 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.020   0.002   PHE A 490 
 TYR   0.026   0.002   TYR A 140 
 ARG   0.002   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  219)
  hydrogen bonds       : angle       4.07812 (  633)
  SS BOND              : bond        0.00419 (    2)
  SS BOND              : angle       0.89476 (    4)
  covalent geometry    : bond        0.00297 ( 4030)
  covalent geometry    : angle       0.63713 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  432 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.5890 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 115
  average time/residue: 0.1216
  time to fit residues: 18.1343
Evaluate side-chains
  118 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    0.2980
   chunk 7 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.157548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.129567 restraints weight = 8227.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133065 restraints weight = 4763.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.135522 restraints weight = 3315.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4032  Z= 0.123
  Angle     :  0.632  12.783   5461  Z= 0.312
  Chirality :  0.042   0.131    597
  Planarity :  0.004   0.032    672
  Dihedral  :  4.739  26.572    511
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 21.04 %
    Favored  : 72.81 %
  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:  1.58 (0.39), residues: 474
  helix:  2.04 (0.33), residues: 230
  sheet:  1.32 (0.64), residues: 61
  loop : -0.32 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 148 
 HIS   0.003   0.000   HIS A 496 
 PHE   0.019   0.002   PHE A 490 
 TYR   0.028   0.002   TYR A 140 
 ARG   0.002   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  219)
  hydrogen bonds       : angle       4.04280 (  633)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       0.87103 (    4)
  covalent geometry    : bond        0.00278 ( 4030)
  covalent geometry    : angle       0.63205 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.8045 (ptp) cc_final: 0.7676 (pmm)
REVERT: A  323 MET cc_start: 0.7485 (mmt) cc_final: 0.7147 (mtt)
REVERT: A  432 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.5929 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 120
  average time/residue: 0.1380
  time to fit residues: 21.1226
Evaluate side-chains
  120 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0870
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7160

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.157261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.129109 restraints weight = 8244.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.132395 restraints weight = 4882.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.134759 restraints weight = 3450.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4032  Z= 0.126
  Angle     :  0.640  15.081   5461  Z= 0.315
  Chirality :  0.042   0.130    597
  Planarity :  0.004   0.040    672
  Dihedral  :  4.679  25.443    511
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 21.99 %
    Favored  : 71.87 %
  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:  1.61 (0.39), residues: 474
  helix:  2.02 (0.33), residues: 230
  sheet:  1.30 (0.63), residues: 61
  loop : -0.22 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.017   0.002   PHE A 490 
 TYR   0.015   0.001   TYR A 140 
 ARG   0.003   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  219)
  hydrogen bonds       : angle       4.04182 (  633)
  SS BOND              : bond        0.00343 (    2)
  SS BOND              : angle       0.77615 (    4)
  covalent geometry    : bond        0.00290 ( 4030)
  covalent geometry    : angle       0.64013 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7256 (t0)
REVERT: A  432 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.5865 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 120
  average time/residue: 0.1241
  time to fit residues: 19.4349
Evaluate side-chains
  126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0770
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.157703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129263 restraints weight = 8154.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.132556 restraints weight = 4918.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.134894 restraints weight = 3485.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4032  Z= 0.131
  Angle     :  0.645  14.804   5461  Z= 0.317
  Chirality :  0.042   0.147    597
  Planarity :  0.004   0.037    672
  Dihedral  :  4.673  24.039    511
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 21.04 %
    Favored  : 72.81 %
  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:  1.68 (0.39), residues: 474
  helix:  2.09 (0.32), residues: 230
  sheet:  1.36 (0.63), residues: 61
  loop : -0.21 (0.49), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.018   0.002   PHE A 490 
 TYR   0.021   0.002   TYR A 392 
 ARG   0.003   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03949 (  219)
  hydrogen bonds       : angle       3.95180 (  633)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       0.71097 (    4)
  covalent geometry    : bond        0.00301 ( 4030)
  covalent geometry    : angle       0.64536 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.8134 (ptp) cc_final: 0.7682 (pmm)
REVERT: A  406 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7273 (t0)
REVERT: A  432 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.5870 (t80)
  outliers start: 26
  outliers final: 22
  residues processed: 122
  average time/residue: 0.1391
  time to fit residues: 21.7661
Evaluate side-chains
  127 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLU
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   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 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.157222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.128168 restraints weight = 8262.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.131694 restraints weight = 4754.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.134219 restraints weight = 3307.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4032  Z= 0.134
  Angle     :  0.654  14.756   5461  Z= 0.323
  Chirality :  0.042   0.130    597
  Planarity :  0.004   0.039    672
  Dihedral  :  4.658  23.517    511
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 21.28 %
    Favored  : 72.58 %
  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:  1.61 (0.38), residues: 474
  helix:  2.03 (0.32), residues: 230
  sheet:  1.28 (0.62), residues: 61
  loop : -0.21 (0.49), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 496 
 PHE   0.021   0.002   PHE A 398 
 TYR   0.018   0.002   TYR A 392 
 ARG   0.002   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  219)
  hydrogen bonds       : angle       3.96154 (  633)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.70965 (    4)
  covalent geometry    : bond        0.00309 ( 4030)
  covalent geometry    : angle       0.65413 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.8191 (ptp) cc_final: 0.7680 (pmm)
REVERT: A  281 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8392 (t0)
REVERT: A  406 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7656 (t0)
REVERT: A  432 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.5987 (t80)
REVERT: A  478 TYR cc_start: 0.8150 (t80) cc_final: 0.7894 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 124
  average time/residue: 0.1306
  time to fit residues: 20.7915
Evaluate side-chains
  133 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  281 ASN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0170
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0770
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.4176

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.158746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.130002 restraints weight = 8306.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.133645 restraints weight = 4744.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.136262 restraints weight = 3259.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4032  Z= 0.126
  Angle     :  0.686  15.245   5461  Z= 0.332
  Chirality :  0.042   0.131    597
  Planarity :  0.004   0.039    672
  Dihedral  :  4.599  22.925    511
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.17 %
    Favored  : 72.10 %
  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:  1.60 (0.39), residues: 474
  helix:  1.96 (0.32), residues: 232
  sheet:  1.01 (0.56), residues: 75
  loop : -0.12 (0.52), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 148 
 HIS   0.003   0.000   HIS A 496 
 PHE   0.023   0.001   PHE A 490 
 TYR   0.019   0.002   TYR A 392 
 ARG   0.002   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  219)
  hydrogen bonds       : angle       3.97319 (  633)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       0.67699 (    4)
  covalent geometry    : bond        0.00289 ( 4030)
  covalent geometry    : angle       0.68575 ( 5457)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.8152 (ptp) cc_final: 0.7655 (pmm)
REVERT: A  104 SER cc_start: 0.8754 (p) cc_final: 0.8375 (p)
REVERT: A  281 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8407 (t0)
REVERT: A  406 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7289 (t0)
REVERT: A  432 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.5938 (t80)
REVERT: A  478 TYR cc_start: 0.8141 (t80) cc_final: 0.7867 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1310
  time to fit residues: 20.2263
Evaluate side-chains
  126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  281 ASN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  477 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0570
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.157584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.128644 restraints weight = 8260.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.132372 restraints weight = 4709.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.134871 restraints weight = 3247.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4032  Z= 0.134
  Angle     :  0.688  15.659   5461  Z= 0.334
  Chirality :  0.042   0.136    597
  Planarity :  0.004   0.040    672
  Dihedral  :  4.584  22.418    511
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 23.64 %
    Favored  : 71.39 %
  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:  1.61 (0.39), residues: 474
  helix:  1.98 (0.33), residues: 232
  sheet:  1.04 (0.55), residues: 75
  loop : -0.16 (0.52), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 153 
 PHE   0.022   0.002   PHE A 490 
 TYR   0.018   0.002   TYR A 392 
 ARG   0.002   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  219)
  hydrogen bonds       : angle       3.98819 (  633)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.66032 (    4)
  covalent geometry    : bond        0.00311 ( 4030)
  covalent geometry    : angle       0.68849 ( 5457)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1741.65 seconds
wall clock time: 30 minutes 49.58 seconds (1849.58 seconds total)