Starting phenix.real_space_refine
on Thu Mar  6 04:01:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hru_34980/03_2025/8hru_34980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hru_34980/03_2025/8hru_34980.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hru_34980/03_2025/8hru_34980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hru_34980/03_2025/8hru_34980.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hru_34980/03_2025/8hru_34980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hru_34980/03_2025/8hru_34980.cif"
  }
  resolution = 3.9
  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=   0.007 sd=   0.066
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      29      5.16       5
     C    3115      2.51       5
     N     806      2.21       5
     O     920      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
  Time building chain proxies: 3.30, per 1000 atoms: 0.68
  Number of scatterers: 4870
  At special positions: 0
  Unit cell: (85.324, 85.324, 71.96, 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      29     16.00
     O     920      8.00
     N     806      7.00
     C    3115      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " 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: 1.15
  Conformation dependent library (CDL) restraints added in 514.0 milliseconds
  

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1130

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      64.5% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 5.108A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A  46 " --> pdb=" O   GLN A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
      removed outlier: 3.730A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ASN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 3.891A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.848A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.578A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 152
      removed outlier: 3.567A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 167
      removed outlier: 3.585A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
      removed outlier: 3.752A  pdb=" N   GLU A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 167 through 172'
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 3.563A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 220 through 249
      removed outlier: 3.952A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.863A  pdb=" N   MET A 249 " --> pdb=" O   ARG A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.606A  pdb=" N   LEU A 278 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 4.057A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ASP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.569A  pdb=" N   PHE A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.895A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.607A  pdb=" N   HIS A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 401
      removed outlier: 3.838A  pdb=" N   HIS A 401 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 413
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 3.709A  pdb=" N   ILE A 421 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.643A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 474 through 482
      removed outlier: 4.260A  pdb=" N   MET A 480 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.955A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.679A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.750A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 4.154A  pdb=" N   GLU A 564 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.793A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.631A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
      removed outlier: 4.361A  pdb=" N   VAL A 132 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A 142 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.845A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 5.838A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    639 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: 1.22

  Time building geometry restraints manager: 1.39 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: 1578
        1.35 -     1.47: 1270
        1.47 -     1.59: 2107
        1.59 -     1.71: 2
        1.71 -     1.83: 50
  Bond restraints: 5007
  Sorted by residual:
  bond pdb=" CG  PRO A 289 "
       pdb=" CD  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.503  1.272  0.231 3.40e-02 8.65e+02 4.61e+01
  bond pdb=" N   PRO A 289 "
       pdb=" CD  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.473  1.535 -0.062 1.40e-02 5.10e+03 1.93e+01
  bond pdb=" CB  PRO A 289 "
       pdb=" CG  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.492  1.686 -0.194 5.00e-02 4.00e+02 1.51e+01
  bond pdb=" CB  PRO A 258 "
       pdb=" CG  PRO A 258 "
    ideal  model  delta    sigma   weight residual
    1.492  1.611 -0.119 5.00e-02 4.00e+02 5.69e+00
  bond pdb=" N   PRO A 289 "
       pdb=" CA  PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.469  1.444  0.024 1.28e-02 6.10e+03 3.62e+00
  ... (remaining 5002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.54: 6730
        3.54 -     7.07: 57
        7.07 -    10.61: 11
       10.61 -    14.15: 3
       14.15 -    17.69: 2
  Bond angle restraints: 6803
  Sorted by residual:
  angle pdb=" CA  PRO A 289 "
        pdb=" N   PRO A 289 "
        pdb=" CD  PRO A 289 "
      ideal   model   delta    sigma   weight residual
     112.00   94.31   17.69 1.40e+00 5.10e-01 1.60e+02
  angle pdb=" N   PRO A 289 "
        pdb=" CD  PRO A 289 "
        pdb=" CG  PRO A 289 "
      ideal   model   delta    sigma   weight residual
     103.20   88.77   14.43 1.50e+00 4.44e-01 9.25e+01
  angle pdb=" CA  PRO A 289 "
        pdb=" CB  PRO A 289 "
        pdb=" CG  PRO A 289 "
      ideal   model   delta    sigma   weight residual
     104.50   92.34   12.16 1.90e+00 2.77e-01 4.09e+01
  angle pdb=" CA  PRO A 258 "
        pdb=" N   PRO A 258 "
        pdb=" CD  PRO A 258 "
      ideal   model   delta    sigma   weight residual
     112.00  105.47    6.53 1.40e+00 5.10e-01 2.18e+01
  angle pdb=" CA  LYS A 353 "
        pdb=" CB  LYS A 353 "
        pdb=" CG  LYS A 353 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  ... (remaining 6798 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 2461
       16.24 -    32.48: 363
       32.48 -    48.71: 101
       48.71 -    64.95: 18
       64.95 -    81.19: 16
  Dihedral angle restraints: 2959
    sinusoidal: 1205
      harmonic: 1754
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.57  -40.57     1      1.00e+01 1.00e-02 2.31e+01
  dihedral pdb=" CA  CYS A 530 "
           pdb=" C   CYS A 530 "
           pdb=" N   GLN A 531 "
           pdb=" CA  GLN A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.21   21.79     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  MET A 579 "
           pdb=" C   MET A 579 "
           pdb=" N   ASN A 580 "
           pdb=" CA  ASN A 580 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.91  -17.09     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 2956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 538
       0.053 -    0.106: 144
       0.106 -    0.159: 23
       0.159 -    0.212: 3
       0.212 -    0.265: 2
  Chirality restraints: 710
  Sorted by residual:
  chirality pdb=" CB  ILE A 151 "
            pdb=" CA  ILE A 151 "
            pdb=" CG1 ILE A 151 "
            pdb=" CG2 ILE A 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CB  THR A 118 "
            pdb=" CA  THR A 118 "
            pdb=" OG1 THR A 118 "
            pdb=" CG2 THR A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CG  LEU A 391 "
            pdb=" CB  LEU A 391 "
            pdb=" CD1 LEU A 391 "
            pdb=" CD2 LEU A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 707 not shown)

  Planarity restraints: 881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 288 "   -0.079 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO A 289 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "    0.055 5.00e-02 4.00e+02   8.22e-02 1.08e+01
        pdb=" N   PRO A 500 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 257 "   -0.042 5.00e-02 4.00e+02   6.07e-02 5.89e+00
        pdb=" N   PRO A 258 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 878 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 62
        2.58 -     3.16: 4222
        3.16 -     3.74: 8348
        3.74 -     4.32: 10856
        4.32 -     4.90: 17365
  Nonbonded interactions: 40853
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 482 "
            pdb=" NH1 ARG A 482 "
     model   vdw
     2.000 3.120
  nonbonded pdb=" O   THR A  92 "
            pdb=" NE2 GLN A  96 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   ALA A 403 "
            pdb=" NE2 GLN A 522 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   THR A 118 "
            pdb=" OG1 THR A 122 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" NH2 ARG A 245 "
            pdb=" O   PHE A 603 "
     model   vdw
     2.226 3.120
  ... (remaining 40848 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:             0.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.130
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
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      :  0.006   0.231   5007  Z= 0.395
  Angle     :  0.980  17.687   6803  Z= 0.547
  Chirality :  0.050   0.265    710
  Planarity :  0.007   0.106    881
  Dihedral  : 17.398  81.191   1820
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 22.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 26.57 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.28 (0.35), residues: 595
  helix: -0.65 (0.28), residues: 334
  sheet: -2.31 (1.19), residues: 10
  loop : -0.87 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 302 
 HIS   0.006   0.001   HIS A 265 
 PHE   0.024   0.002   PHE A 588 
 TYR   0.034   0.002   TYR A 521 
 ARG   0.011   0.001   ARG A 482 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7125 (mmp) cc_final: 0.6647 (mmp)
REVERT: A  350 ASP cc_start: 0.8261 (t0) cc_final: 0.6468 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1602
  time to fit residues: 20.2456
Evaluate side-chains
  87 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 34 optimal weight:   30.0000
   chunk 53 optimal weight:    5.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.132334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.113846 restraints weight = 15834.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.116868 restraints weight = 10169.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.119131 restraints weight = 7293.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5007  Z= 0.234
  Angle     :  0.709   9.676   6803  Z= 0.352
  Chirality :  0.045   0.160    710
  Planarity :  0.005   0.070    881
  Dihedral  :  4.840  20.138    642
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 21.82 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.35), residues: 595
  helix: -0.35 (0.28), residues: 347
  sheet: -2.18 (1.40), residues: 10
  loop : -0.76 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 477 
 HIS   0.005   0.001   HIS A 265 
 PHE   0.017   0.002   PHE A 525 
 TYR   0.022   0.002   TYR A 521 
 ARG   0.007   0.001   ARG A 482 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 LYS cc_start: 0.6017 (mttt) cc_final: 0.5390 (mttt)
  outliers start: 18
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1367
  time to fit residues: 20.0382
Evaluate side-chains
  91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   chunk 54 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 GLN
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.128916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.111012 restraints weight = 16020.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.113931 restraints weight = 10319.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.115968 restraints weight = 7421.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5007  Z= 0.244
  Angle     :  0.706  12.737   6803  Z= 0.351
  Chirality :  0.046   0.167    710
  Planarity :  0.004   0.046    881
  Dihedral  :  4.860  19.725    642
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.63 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.36), residues: 595
  helix: -0.26 (0.29), residues: 342
  sheet: -2.19 (1.52), residues: 10
  loop : -0.57 (0.45), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A 239 
 PHE   0.017   0.002   PHE A 512 
 TYR   0.034   0.002   TYR A 521 
 ARG   0.003   0.001   ARG A 482 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.9061 (t80) cc_final: 0.8860 (t80)
REVERT: A  168 TRP cc_start: 0.7794 (t-100) cc_final: 0.6367 (t-100)
REVERT: A  237 TYR cc_start: 0.6958 (t80) cc_final: 0.6141 (t80)
REVERT: A  481 LYS cc_start: 0.6347 (mttt) cc_final: 0.6047 (mttt)
  outliers start: 21
  outliers final: 12
  residues processed: 114
  average time/residue: 0.1518
  time to fit residues: 22.7150
Evaluate side-chains
  104 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    2.8086

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.130088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.111933 restraints weight = 16009.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.114948 restraints weight = 10365.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.117032 restraints weight = 7426.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5007  Z= 0.205
  Angle     :  0.682  12.815   6803  Z= 0.335
  Chirality :  0.045   0.168    710
  Planarity :  0.004   0.046    881
  Dihedral  :  4.831  18.938    642
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.82 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.36), residues: 595
  helix: -0.08 (0.29), residues: 344
  sheet: -2.00 (1.60), residues: 10
  loop : -0.38 (0.45), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 594 
 HIS   0.002   0.001   HIS A 417 
 PHE   0.015   0.002   PHE A 588 
 TYR   0.030   0.002   TYR A 521 
 ARG   0.005   0.001   ARG A 482 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.9033 (t80) cc_final: 0.8824 (t80)
REVERT: A  168 TRP cc_start: 0.7914 (t-100) cc_final: 0.7032 (t-100)
REVERT: A  237 TYR cc_start: 0.6962 (t80) cc_final: 0.6279 (t80)
REVERT: A  525 PHE cc_start: 0.7568 (m-80) cc_final: 0.6839 (m-80)
REVERT: A  579 MET cc_start: 0.7090 (ppp) cc_final: 0.6859 (ppp)
  outliers start: 22
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1456
  time to fit residues: 21.6591
Evaluate side-chains
  103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0980
   chunk 2 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 41 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    4.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 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 = 0.4301 r_free = 0.4301 target = 0.127571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.109171 restraints weight = 16170.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.112251 restraints weight = 10385.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.114382 restraints weight = 7442.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5007  Z= 0.260
  Angle     :  0.725  10.809   6803  Z= 0.358
  Chirality :  0.046   0.178    710
  Planarity :  0.004   0.046    881
  Dihedral  :  4.954  18.446    642
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 19.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.48 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.36), residues: 595
  helix:  0.02 (0.29), residues: 344
  sheet: -2.05 (1.63), residues: 10
  loop : -0.41 (0.45), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP A 271 
 HIS   0.002   0.001   HIS A 228 
 PHE   0.026   0.002   PHE A 588 
 TYR   0.023   0.002   TYR A 521 
 ARG   0.008   0.001   ARG A 482 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.9106 (t80) cc_final: 0.8873 (t80)
REVERT: A   67 ASP cc_start: 0.8776 (m-30) cc_final: 0.8159 (p0)
REVERT: A  237 TYR cc_start: 0.7292 (t80) cc_final: 0.6735 (t80)
REVERT: A  390 PHE cc_start: 0.7731 (t80) cc_final: 0.6482 (t80)
REVERT: A  481 LYS cc_start: 0.7106 (mttt) cc_final: 0.6359 (ptpp)
REVERT: A  568 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7755 (tt)
REVERT: A  579 MET cc_start: 0.6985 (ppp) cc_final: 0.6722 (ppp)
  outliers start: 22
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1379
  time to fit residues: 19.4967
Evaluate side-chains
  104 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0470
   chunk 18 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    5.4086

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 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 = 0.4259 r_free = 0.4259 target = 0.124354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.105844 restraints weight = 16415.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.108808 restraints weight = 10540.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.110827 restraints weight = 7545.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5007  Z= 0.312
  Angle     :  0.783  10.836   6803  Z= 0.394
  Chirality :  0.048   0.179    710
  Planarity :  0.005   0.050    881
  Dihedral  :  5.189  19.614    642
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 22.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 22.96 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.36), residues: 595
  helix: -0.15 (0.28), residues: 348
  sheet: -2.16 (1.43), residues: 12
  loop : -0.37 (0.46), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP A 271 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.017   0.002   PHE A 588 
 TYR   0.028   0.002   TYR A 521 
 ARG   0.005   0.001   ARG A 482 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9227 (mttt) cc_final: 0.8865 (mmtt)
REVERT: A  152 MET cc_start: 0.8188 (mmp) cc_final: 0.7862 (mmp)
REVERT: A  481 LYS cc_start: 0.6996 (mttt) cc_final: 0.6372 (ptpt)
REVERT: A  525 PHE cc_start: 0.7774 (m-10) cc_final: 0.7142 (m-80)
REVERT: A  568 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7814 (tt)
  outliers start: 26
  outliers final: 20
  residues processed: 111
  average time/residue: 0.1517
  time to fit residues: 22.2441
Evaluate side-chains
  102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0050
   chunk 53 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   overall best weight:    1.6000

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.130545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.112562 restraints weight = 16224.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.115533 restraints weight = 10556.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.117675 restraints weight = 7565.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5007  Z= 0.189
  Angle     :  0.722  10.666   6803  Z= 0.347
  Chirality :  0.045   0.183    710
  Planarity :  0.004   0.047    881
  Dihedral  :  4.784  18.924    642
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 24.86 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.36), residues: 595
  helix:  0.11 (0.28), residues: 344
  sheet: -1.97 (1.40), residues: 12
  loop : -0.44 (0.46), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 594 
 HIS   0.003   0.001   HIS A 417 
 PHE   0.015   0.002   PHE A 512 
 TYR   0.033   0.002   TYR A 521 
 ARG   0.007   0.001   ARG A 460 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9198 (mttt) cc_final: 0.8854 (mmtt)
REVERT: A   67 ASP cc_start: 0.8698 (m-30) cc_final: 0.8154 (p0)
REVERT: A  168 TRP cc_start: 0.7802 (t-100) cc_final: 0.7594 (t-100)
REVERT: A  481 LYS cc_start: 0.6975 (mttt) cc_final: 0.6193 (ptpp)
REVERT: A  579 MET cc_start: 0.7078 (ppp) cc_final: 0.6810 (ppp)
  outliers start: 16
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1565
  time to fit residues: 21.5235
Evaluate side-chains
  100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    4.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 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 = 0.4292 r_free = 0.4292 target = 0.126828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.108625 restraints weight = 16763.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.111435 restraints weight = 10950.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.113488 restraints weight = 8016.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5007  Z= 0.275
  Angle     :  0.763  10.548   6803  Z= 0.378
  Chirality :  0.047   0.214    710
  Planarity :  0.004   0.047    881
  Dihedral  :  5.022  18.066    642
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 21.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 25.43 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.36), residues: 595
  helix:  0.05 (0.29), residues: 343
  sheet: -2.06 (1.36), residues: 12
  loop : -0.50 (0.45), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A 594 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.018   0.002   PHE A 512 
 TYR   0.026   0.002   TYR A 521 
 ARG   0.010   0.001   ARG A 460 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9194 (mttt) cc_final: 0.8882 (mmtt)
REVERT: A   62 MET cc_start: 0.8793 (ptm) cc_final: 0.8469 (ptt)
REVERT: A   67 ASP cc_start: 0.8677 (m-30) cc_final: 0.8082 (p0)
REVERT: A  123 MET cc_start: 0.8080 (mmp) cc_final: 0.7849 (mmt)
REVERT: A  152 MET cc_start: 0.8096 (mmp) cc_final: 0.7676 (mmp)
REVERT: A  243 TYR cc_start: 0.7981 (t80) cc_final: 0.7547 (t80)
REVERT: A  525 PHE cc_start: 0.7667 (m-10) cc_final: 0.7073 (m-80)
  outliers start: 18
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1561
  time to fit residues: 19.9266
Evaluate side-chains
  102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 11 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 46 optimal weight:    0.5980
   chunk 18 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.129917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.111490 restraints weight = 16540.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.114491 restraints weight = 10761.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.116669 restraints weight = 7747.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5007  Z= 0.205
  Angle     :  0.731  11.054   6803  Z= 0.354
  Chirality :  0.045   0.201    710
  Planarity :  0.004   0.045    881
  Dihedral  :  4.744  18.221    642
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 26.76 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.37), residues: 595
  helix:  0.09 (0.29), residues: 342
  sheet: -1.92 (1.34), residues: 12
  loop : -0.24 (0.47), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 168 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.030   0.002   TYR A 521 
 ARG   0.005   0.001   ARG A 460 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9213 (mttt) cc_final: 0.8901 (mmtt)
REVERT: A   62 MET cc_start: 0.8842 (ptm) cc_final: 0.8552 (ptt)
REVERT: A   67 ASP cc_start: 0.8730 (m-30) cc_final: 0.8157 (p0)
REVERT: A  123 MET cc_start: 0.8194 (mmp) cc_final: 0.7930 (mmt)
REVERT: A  152 MET cc_start: 0.8085 (mmp) cc_final: 0.7710 (mmp)
REVERT: A  228 HIS cc_start: 0.8782 (t70) cc_final: 0.7903 (t70)
REVERT: A  243 TYR cc_start: 0.8181 (t80) cc_final: 0.7788 (t80)
REVERT: A  481 LYS cc_start: 0.7226 (mttt) cc_final: 0.6800 (pttm)
REVERT: A  521 TYR cc_start: 0.6513 (m-80) cc_final: 0.6156 (m-10)
REVERT: A  525 PHE cc_start: 0.7727 (m-10) cc_final: 0.7143 (m-80)
  outliers start: 16
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1456
  time to fit residues: 19.4452
Evaluate side-chains
  103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 ASP
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0980
   chunk 40 optimal weight:    0.7980
   chunk 15 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
A 154 ASN
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.135016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.116609 restraints weight = 16038.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.119785 restraints weight = 10578.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.121903 restraints weight = 7639.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5007  Z= 0.180
  Angle     :  0.727  11.033   6803  Z= 0.352
  Chirality :  0.044   0.204    710
  Planarity :  0.004   0.051    881
  Dihedral  :  4.504  18.400    642
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.13 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.36), residues: 595
  helix:  0.09 (0.29), residues: 341
  sheet:  None (None), residues: 0
  loop : -0.34 (0.44), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP A 168 
 HIS   0.005   0.001   HIS A 417 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.034   0.002   TYR A 521 
 ARG   0.004   0.000   ARG A 357 

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9179 (mttt) cc_final: 0.8883 (mmtt)
REVERT: A   62 MET cc_start: 0.8737 (ptm) cc_final: 0.8464 (ptt)
REVERT: A   67 ASP cc_start: 0.8529 (m-30) cc_final: 0.8177 (m-30)
REVERT: A  123 MET cc_start: 0.7959 (mmp) cc_final: 0.7710 (mmt)
REVERT: A  152 MET cc_start: 0.8094 (mmp) cc_final: 0.7831 (mmp)
REVERT: A  169 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8003 (ptp-170)
REVERT: A  174 LYS cc_start: 0.8905 (mptt) cc_final: 0.8576 (mmtp)
REVERT: A  190 MET cc_start: 0.6481 (tpt) cc_final: 0.6177 (tpt)
REVERT: A  228 HIS cc_start: 0.8690 (t70) cc_final: 0.7704 (t70)
REVERT: A  237 TYR cc_start: 0.7335 (t80) cc_final: 0.6613 (t80)
REVERT: A  243 TYR cc_start: 0.8055 (t80) cc_final: 0.7599 (t80)
REVERT: A  270 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5629 (tpp)
REVERT: A  462 MET cc_start: 0.5588 (pmm) cc_final: 0.5189 (pmm)
  outliers start: 16
  outliers final: 11
  residues processed: 107
  average time/residue: 0.1598
  time to fit residues: 22.3445
Evaluate side-chains
  100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 30 optimal weight:    8.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.134807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.115872 restraints weight = 16223.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.119027 restraints weight = 10700.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.121134 restraints weight = 7695.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5007  Z= 0.188
  Angle     :  0.755  11.201   6803  Z= 0.365
  Chirality :  0.044   0.193    710
  Planarity :  0.004   0.042    881
  Dihedral  :  4.431  18.369    642
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.70 %
    Favored  : 69.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.36), residues: 595
  helix:  0.09 (0.29), residues: 342
  sheet: -0.78 (1.39), residues: 12
  loop : -0.34 (0.45), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP A 168 
 HIS   0.014   0.001   HIS A 417 
 PHE   0.014   0.001   PHE A 390 
 TYR   0.033   0.002   TYR A 521 
 ARG   0.006   0.001   ARG A 357 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1593.82 seconds
wall clock time: 28 minutes 32.35 seconds (1712.35 seconds total)