Starting phenix.real_space_refine
on Sat May 10 07:29:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wua_37852/05_2025/8wua_37852.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wua_37852/05_2025/8wua_37852.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wua_37852/05_2025/8wua_37852.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wua_37852/05_2025/8wua_37852.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wua_37852/05_2025/8wua_37852.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wua_37852/05_2025/8wua_37852.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.056
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      38      5.16       5
     C    3622      2.51       5
     N     888      2.21       5
     O     946      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5494
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 5494
          Classifications: {'peptide': 675}
          Link IDs: {'PTRANS': 26, 'TRANS': 648}
          Chain breaks: 1
  Time building chain proxies: 3.61, per 1000 atoms: 0.66
  Number of scatterers: 5494
  At special positions: 0
  Unit cell: (91.1257, 96.6152, 92.2236, 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      38     16.00
     O     946      8.00
     N     888      7.00
     C    3622      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  32 " - pdb=" SG  CYS A 546 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 315 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 624.5 milliseconds
  

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1292

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 2 sheets defined
      65.2% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 18
      removed outlier: 4.130A  pdb=" N   ARG A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 21
      No H-bonds generated for 'chain 'A' and resid 19 through 21'
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 49 through 75
      removed outlier: 3.712A  pdb=" N   VAL A  53 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 123
      removed outlier: 4.001A  pdb=" N   ILE A 120 " --> pdb=" O   TRP A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 132
    Processing helix  chain 'A' and resid 134 through 158
      removed outlier: 3.791A  pdb=" N   HIS A 138 " --> pdb=" O   GLU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 167
      removed outlier: 3.822A  pdb=" N   VAL A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 182
      removed outlier: 3.749A  pdb=" N   THR A 181 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 219
      removed outlier: 3.793A  pdb=" N   HIS A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LEU A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 205 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 252
    Processing helix  chain 'A' and resid 266 through 294
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 4.116A  pdb=" N   PHE A 307 " --> pdb=" O   CYS A 304 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   CYS A 308 " --> pdb=" O   GLY A 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 308'
    Processing helix  chain 'A' and resid 320 through 341
      removed outlier: 3.651A  pdb=" N   ARG A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 345
      removed outlier: 3.753A  pdb=" N   GLN A 345 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 342 through 345'
    Processing helix  chain 'A' and resid 357 through 365
    Processing helix  chain 'A' and resid 415 through 445
      removed outlier: 3.915A  pdb=" N   TRP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   THR A 428 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 466 through 491
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 494 through 515
      removed outlier: 4.153A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   GLN A 500 " --> pdb=" O   SER A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 534
    Processing helix  chain 'A' and resid 550 through 553
    Processing helix  chain 'A' and resid 554 through 565
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 574 through 587
    Processing helix  chain 'A' and resid 594 through 599
      removed outlier: 3.767A  pdb=" N   LYS A 598 " --> pdb=" O   ARG A 594 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN A 599 " --> pdb=" O   ARG A 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 594 through 599'
    Processing helix  chain 'A' and resid 606 through 624
    Processing helix  chain 'A' and resid 630 through 650
      removed outlier: 3.984A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 673
      removed outlier: 3.598A  pdb=" N   ALA A 673 " --> pdb=" O   ASN A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 690
    Processing helix  chain 'A' and resid 694 through 710
      removed outlier: 3.588A  pdb=" N   LEU A 698 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 717
      removed outlier: 4.042A  pdb=" N   PHE A 717 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 262
      removed outlier: 3.814A  pdb=" N   ILE A 232 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL A 352 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   THR A 396 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299

    301 hydrogen bonds defined for protein.
    891 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: 1.45

  Time building geometry restraints manager: 1.51 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: 1673
        1.35 -     1.46: 1428
        1.46 -     1.58: 2487
        1.58 -     1.70: 2
        1.70 -     1.81: 53
  Bond restraints: 5643
  Sorted by residual:
  bond pdb=" CB  PRO A 439 "
       pdb=" CG  PRO A 439 "
    ideal  model  delta    sigma   weight residual
    1.492  1.654 -0.162 5.00e-02 4.00e+02 1.05e+01
  bond pdb=" CB  PRO A 576 "
       pdb=" CG  PRO A 576 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.88e+00
  bond pdb=" N   PRO A 439 "
       pdb=" CD  PRO A 439 "
    ideal  model  delta    sigma   weight residual
    1.473  1.498 -0.025 1.40e-02 5.10e+03 3.15e+00
  bond pdb=" N   PRO A 439 "
       pdb=" CA  PRO A 439 "
    ideal  model  delta    sigma   weight residual
    1.470  1.449  0.021 1.34e-02 5.57e+03 2.55e+00
  bond pdb=" CG  PRO A 439 "
       pdb=" CD  PRO A 439 "
    ideal  model  delta    sigma   weight residual
    1.503  1.450  0.053 3.40e-02 8.65e+02 2.46e+00
  ... (remaining 5638 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.23: 7602
        3.23 -     6.45: 44
        6.45 -     9.68: 12
        9.68 -    12.91: 5
       12.91 -    16.14: 2
  Bond angle restraints: 7665
  Sorted by residual:
  angle pdb=" CA  PRO A 439 "
        pdb=" N   PRO A 439 "
        pdb=" CD  PRO A 439 "
      ideal   model   delta    sigma   weight residual
     112.00   95.86   16.14 1.40e+00 5.10e-01 1.33e+02
  angle pdb=" CA  PRO A 576 "
        pdb=" N   PRO A 576 "
        pdb=" CD  PRO A 576 "
      ideal   model   delta    sigma   weight residual
     112.00  101.38   10.62 1.40e+00 5.10e-01 5.75e+01
  angle pdb=" N   PRO A 439 "
        pdb=" CD  PRO A 439 "
        pdb=" CG  PRO A 439 "
      ideal   model   delta    sigma   weight residual
     103.20   95.89    7.31 1.50e+00 4.44e-01 2.38e+01
  angle pdb=" CA  MET A 327 "
        pdb=" CB  MET A 327 "
        pdb=" CG  MET A 327 "
      ideal   model   delta    sigma   weight residual
     114.10  122.70   -8.60 2.00e+00 2.50e-01 1.85e+01
  angle pdb=" CA  LEU A 471 "
        pdb=" CB  LEU A 471 "
        pdb=" CG  LEU A 471 "
      ideal   model   delta    sigma   weight residual
     116.30  130.57  -14.27 3.50e+00 8.16e-02 1.66e+01
  ... (remaining 7660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 2943
       18.00 -    36.00: 273
       36.00 -    54.00: 85
       54.00 -    72.00: 5
       72.00 -    90.00: 7
  Dihedral angle restraints: 3313
    sinusoidal: 1321
      harmonic: 1992
  Sorted by residual:
  dihedral pdb=" CB  CYS A 308 "
           pdb=" SG  CYS A 308 "
           pdb=" SG  CYS A 315 "
           pdb=" CB  CYS A 315 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -20.15  -65.85     1      1.00e+01 1.00e-02 5.67e+01
  dihedral pdb=" CB  CYS A  32 "
           pdb=" SG  CYS A  32 "
           pdb=" SG  CYS A 546 "
           pdb=" CB  CYS A 546 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.01   56.99     1      1.00e+01 1.00e-02 4.37e+01
  dihedral pdb=" CA  ASP A 366 "
           pdb=" C   ASP A 366 "
           pdb=" N   PHE A 367 "
           pdb=" CA  PHE A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.76  -18.24     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 3310 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 752
       0.057 -    0.115: 115
       0.115 -    0.172: 5
       0.172 -    0.229: 1
       0.229 -    0.286: 2
  Chirality restraints: 875
  Sorted by residual:
  chirality pdb=" CA  PRO A 439 "
            pdb=" N   PRO A 439 "
            pdb=" C   PRO A 439 "
            pdb=" CB  PRO A 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" CA  PRO A 576 "
            pdb=" N   PRO A 576 "
            pdb=" C   PRO A 576 "
            pdb=" CB  PRO A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  MET A 327 "
            pdb=" N   MET A 327 "
            pdb=" C   MET A 327 "
            pdb=" CB  MET A 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.42e-01
  ... (remaining 872 not shown)

  Planarity restraints: 941
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 438 "   -0.084 5.00e-02 4.00e+02   1.14e-01 2.09e+01
        pdb=" N   PRO A 439 "    0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO A 439 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 439 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 575 "   -0.070 5.00e-02 4.00e+02   9.88e-02 1.56e+01
        pdb=" N   PRO A 576 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A 576 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 576 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 529 "   -0.017 2.00e-02 2.50e+03   1.94e-02 6.59e+00
        pdb=" CG  PHE A 529 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 529 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 529 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 529 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 529 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 529 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 938 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 65
        2.66 -     3.22: 5218
        3.22 -     3.78: 8354
        3.78 -     4.34: 10099
        4.34 -     4.90: 16539
  Nonbonded interactions: 40275
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 531 "
            pdb=" OG1 THR A 536 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   ALA A 694 "
            pdb=" OG1 THR A 697 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" NE1 TRP A 418 "
            pdb=" OE2 GLU A 490 "
     model   vdw
     2.378 3.120
  nonbonded pdb=" NZ  LYS A 371 "
            pdb=" O   VAL A 397 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" OE1 GLN A 465 "
            pdb=" ND2 ASN A 558 "
     model   vdw
     2.383 3.120
  ... (remaining 40270 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:             0.990
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.570
  Find NCS groups from input model:        0.060
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5848
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      :  0.004   0.162   5645  Z= 0.137
  Angle     :  0.750  16.137   7669  Z= 0.376
  Chirality :  0.041   0.286    875
  Planarity :  0.006   0.114    941
  Dihedral  : 15.346  89.998   2015
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 23.03 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.33), residues: 671
  helix:  1.41 (0.27), residues: 399
  sheet:  0.65 (1.91), residues: 10
  loop : -1.80 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 131 
 HIS   0.003   0.001   HIS A 648 
 PHE   0.045   0.001   PHE A 529 
 TYR   0.014   0.001   TYR A 203 
 ARG   0.003   0.000   ARG A 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09075 (  301)
  hydrogen bonds       : angle       4.45219 (  891)
  SS BOND              : bond        0.00072 (    2)
  SS BOND              : angle       0.32475 (    4)
  covalent geometry    : bond        0.00359 ( 5643)
  covalent geometry    : angle       0.75018 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 MET cc_start: 0.6903 (mpp) cc_final: 0.6329 (pmm)
REVERT: A  413 ILE cc_start: 0.6200 (mt) cc_final: 0.5987 (pt)
REVERT: A  513 MET cc_start: 0.8271 (tmm) cc_final: 0.7846 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 78
  average time/residue: 0.1395
  time to fit residues: 15.2510
Evaluate side-chains
  74 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 648 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.170666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.144063 restraints weight = 14617.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.147906 restraints weight = 7820.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.150357 restraints weight = 5166.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6444
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5645  Z= 0.123
  Angle     :  0.603  11.036   7669  Z= 0.290
  Chirality :  0.040   0.142    875
  Planarity :  0.004   0.047    941
  Dihedral  :  4.401  46.630    733
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 19.57 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.34), residues: 671
  helix:  1.34 (0.27), residues: 407
  sheet:  0.21 (1.42), residues: 17
  loop : -2.02 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 395 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.033   0.001   PHE A 529 
 TYR   0.016   0.001   TYR A 323 
 ARG   0.005   0.001   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03268 (  301)
  hydrogen bonds       : angle       3.86361 (  891)
  SS BOND              : bond        0.00154 (    2)
  SS BOND              : angle       0.43772 (    4)
  covalent geometry    : bond        0.00271 ( 5643)
  covalent geometry    : angle       0.60342 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.4860 (ptm160) cc_final: 0.4152 (tpt170)
REVERT: A  265 ASN cc_start: 0.8302 (t0) cc_final: 0.7987 (t0)
REVERT: A  327 MET cc_start: 0.6854 (mpp) cc_final: 0.6552 (ptp)
REVERT: A  413 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6832 (pt)
REVERT: A  437 THR cc_start: 0.6426 (m) cc_final: 0.6218 (t)
REVERT: A  614 MET cc_start: 0.7905 (ttm) cc_final: 0.7684 (ttm)
REVERT: A  627 THR cc_start: 0.7983 (m) cc_final: 0.7433 (p)
REVERT: A  683 TYR cc_start: 0.7192 (t80) cc_final: 0.6978 (t80)
  outliers start: 24
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1184
  time to fit residues: 17.1196
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  435 PHE
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.156787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.127337 restraints weight = 14633.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.131084 restraints weight = 7831.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.133485 restraints weight = 5217.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5645  Z= 0.133
  Angle     :  0.637  10.560   7669  Z= 0.302
  Chirality :  0.041   0.147    875
  Planarity :  0.004   0.036    941
  Dihedral  :  4.032  35.375    731
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 20.72 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.34), residues: 671
  helix:  1.42 (0.27), residues: 407
  sheet: -0.13 (1.41), residues: 17
  loop : -1.97 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 395 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.038   0.001   PHE A 529 
 TYR   0.013   0.001   TYR A 362 
 ARG   0.004   0.001   ARG A 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  301)
  hydrogen bonds       : angle       3.79615 (  891)
  SS BOND              : bond        0.00008 (    2)
  SS BOND              : angle       0.22948 (    4)
  covalent geometry    : bond        0.00294 ( 5643)
  covalent geometry    : angle       0.63711 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4455 (ptm160) cc_final: 0.3934 (tpt170)
REVERT: A  270 ILE cc_start: 0.7873 (mm) cc_final: 0.7551 (mm)
REVERT: A  327 MET cc_start: 0.7176 (mpp) cc_final: 0.6878 (ptp)
REVERT: A  413 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7355 (pt)
REVERT: A  449 PHE cc_start: 0.7876 (m-80) cc_final: 0.7399 (m-80)
REVERT: A  544 LEU cc_start: 0.8165 (pt) cc_final: 0.7697 (pp)
REVERT: A  545 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8314 (pp20)
REVERT: A  683 TYR cc_start: 0.7676 (t80) cc_final: 0.7197 (t80)
  outliers start: 26
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1314
  time to fit residues: 22.2303
Evaluate side-chains
  104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  545 GLU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  682 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 604 GLN
A 664 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.146133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.114907 restraints weight = 14251.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.118877 restraints weight = 7207.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.121425 restraints weight = 4646.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.5015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5645  Z= 0.131
  Angle     :  0.597  10.471   7669  Z= 0.288
  Chirality :  0.040   0.131    875
  Planarity :  0.003   0.037    941
  Dihedral  :  3.667  16.917    729
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.38 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.34), residues: 671
  helix:  1.50 (0.27), residues: 410
  sheet: -0.43 (1.35), residues: 17
  loop : -2.05 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 473 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.035   0.001   PHE A 529 
 TYR   0.009   0.001   TYR A 203 
 ARG   0.002   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  301)
  hydrogen bonds       : angle       3.68540 (  891)
  SS BOND              : bond        0.00036 (    2)
  SS BOND              : angle       0.36623 (    4)
  covalent geometry    : bond        0.00286 ( 5643)
  covalent geometry    : angle       0.59703 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4541 (ptm160) cc_final: 0.3932 (tpt170)
REVERT: A  270 ILE cc_start: 0.8259 (mm) cc_final: 0.7932 (mm)
REVERT: A  413 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7476 (pt)
REVERT: A  544 LEU cc_start: 0.8314 (pt) cc_final: 0.7781 (pp)
  outliers start: 28
  outliers final: 17
  residues processed: 104
  average time/residue: 0.1146
  time to fit residues: 17.2593
Evaluate side-chains
  105 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  435 PHE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0000
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.144083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.113882 restraints weight = 13597.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.117684 restraints weight = 6885.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.120191 restraints weight = 4427.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.5580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5645  Z= 0.118
  Angle     :  0.610  10.468   7669  Z= 0.290
  Chirality :  0.040   0.202    875
  Planarity :  0.003   0.035    941
  Dihedral  :  3.640  18.630    729
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.37 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.34), residues: 671
  helix:  1.58 (0.27), residues: 407
  sheet: -0.24 (1.29), residues: 17
  loop : -2.03 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 131 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.043   0.001   PHE A 529 
 TYR   0.012   0.001   TYR A 323 
 ARG   0.003   0.000   ARG A 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  301)
  hydrogen bonds       : angle       3.64836 (  891)
  SS BOND              : bond        0.00019 (    2)
  SS BOND              : angle       0.38065 (    4)
  covalent geometry    : bond        0.00259 ( 5643)
  covalent geometry    : angle       0.60971 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.4514 (ptm160) cc_final: 0.3956 (tpt170)
REVERT: A  270 ILE cc_start: 0.8395 (mm) cc_final: 0.8066 (mm)
REVERT: A  413 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7643 (pt)
REVERT: A  427 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7057 (t80)
  outliers start: 28
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1290
  time to fit residues: 19.2290
Evaluate side-chains
  102 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 4 optimal weight:    0.3980
   chunk 42 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.143038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.112838 restraints weight = 13520.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.116691 restraints weight = 6764.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.119174 restraints weight = 4323.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6676
moved from start:          0.5999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5645  Z= 0.112
  Angle     :  0.612   9.791   7669  Z= 0.294
  Chirality :  0.040   0.153    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.591  17.065    729
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 22.70 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.34), residues: 671
  helix:  1.55 (0.27), residues: 412
  sheet: -0.15 (1.31), residues: 17
  loop : -2.04 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 131 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.045   0.001   PHE A 529 
 TYR   0.019   0.001   TYR A 559 
 ARG   0.001   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03379 (  301)
  hydrogen bonds       : angle       3.68891 (  891)
  SS BOND              : bond        0.00030 (    2)
  SS BOND              : angle       0.42300 (    4)
  covalent geometry    : bond        0.00244 ( 5643)
  covalent geometry    : angle       0.61212 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4494 (ptm160) cc_final: 0.3995 (tpt170)
REVERT: A  270 ILE cc_start: 0.8411 (mm) cc_final: 0.8096 (mm)
REVERT: A  413 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7643 (pt)
REVERT: A  427 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6990 (t80)
REVERT: A  627 THR cc_start: 0.7863 (m) cc_final: 0.7315 (p)
REVERT: A  670 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8159 (tm130)
  outliers start: 29
  outliers final: 21
  residues processed: 109
  average time/residue: 0.1280
  time to fit residues: 19.8022
Evaluate side-chains
  109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  670 GLN
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.139099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.108989 restraints weight = 13682.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.112735 restraints weight = 6790.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.115116 restraints weight = 4327.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.6563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5645  Z= 0.127
  Angle     :  0.631  10.908   7669  Z= 0.303
  Chirality :  0.041   0.152    875
  Planarity :  0.003   0.035    941
  Dihedral  :  3.729  18.241    729
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 23.52 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.34), residues: 671
  helix:  1.53 (0.27), residues: 412
  sheet:  0.02 (1.35), residues: 17
  loop : -1.99 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 473 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.045   0.001   PHE A 529 
 TYR   0.022   0.001   TYR A 507 
 ARG   0.002   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03695 (  301)
  hydrogen bonds       : angle       3.70955 (  891)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.60732 (    4)
  covalent geometry    : bond        0.00284 ( 5643)
  covalent geometry    : angle       0.63095 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4390 (ptm160) cc_final: 0.3792 (tpt170)
REVERT: A  270 ILE cc_start: 0.8395 (mm) cc_final: 0.8099 (mm)
REVERT: A  427 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7036 (t80)
REVERT: A  496 SER cc_start: 0.8966 (m) cc_final: 0.8540 (p)
REVERT: A  670 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8049 (tp40)
  outliers start: 33
  outliers final: 25
  residues processed: 112
  average time/residue: 0.1238
  time to fit residues: 19.5723
Evaluate side-chains
  113 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  670 GLN
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0060
   chunk 54 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0770
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.3954

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.140945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.111042 restraints weight = 13751.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.114858 restraints weight = 6823.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.117292 restraints weight = 4352.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.6715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5645  Z= 0.111
  Angle     :  0.646  10.775   7669  Z= 0.305
  Chirality :  0.041   0.184    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.674  16.786    729
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.67 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.34), residues: 671
  helix:  1.51 (0.26), residues: 413
  sheet:  0.05 (1.35), residues: 17
  loop : -1.99 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 531 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.046   0.001   PHE A 529 
 TYR   0.015   0.001   TYR A 559 
 ARG   0.001   0.000   ARG A 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  301)
  hydrogen bonds       : angle       3.71377 (  891)
  SS BOND              : bond        0.00042 (    2)
  SS BOND              : angle       0.51505 (    4)
  covalent geometry    : bond        0.00236 ( 5643)
  covalent geometry    : angle       0.64560 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4151 (ptm160) cc_final: 0.3878 (tpt170)
REVERT: A  327 MET cc_start: 0.7241 (mpp) cc_final: 0.6988 (pmm)
REVERT: A  427 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7008 (t80)
REVERT: A  496 SER cc_start: 0.8898 (m) cc_final: 0.8511 (p)
REVERT: A  670 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8233 (tm130)
  outliers start: 24
  outliers final: 20
  residues processed: 104
  average time/residue: 0.1275
  time to fit residues: 18.9602
Evaluate side-chains
  104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  670 GLN
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 57 optimal weight:    0.0070
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.139194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.109173 restraints weight = 13891.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.112944 restraints weight = 6895.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.115347 restraints weight = 4390.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.7014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5645  Z= 0.117
  Angle     :  0.641   9.943   7669  Z= 0.302
  Chirality :  0.041   0.173    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.746  17.696    729
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 24.01 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.34), residues: 671
  helix:  1.51 (0.27), residues: 413
  sheet:  0.02 (1.35), residues: 17
  loop : -1.97 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 531 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.048   0.001   PHE A 529 
 TYR   0.018   0.001   TYR A 559 
 ARG   0.002   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03521 (  301)
  hydrogen bonds       : angle       3.71890 (  891)
  SS BOND              : bond        0.00022 (    2)
  SS BOND              : angle       0.47206 (    4)
  covalent geometry    : bond        0.00261 ( 5643)
  covalent geometry    : angle       0.64096 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4307 (ptm160) cc_final: 0.4065 (tpt170)
REVERT: A  156 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8049 (mm)
REVERT: A  427 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7034 (t80)
REVERT: A  496 SER cc_start: 0.8902 (m) cc_final: 0.8502 (p)
REVERT: A  585 MET cc_start: 0.1911 (tmm) cc_final: 0.0389 (mmt)
REVERT: A  708 ILE cc_start: 0.8892 (mm) cc_final: 0.8679 (pt)
  outliers start: 26
  outliers final: 21
  residues processed: 104
  average time/residue: 0.1254
  time to fit residues: 18.7099
Evaluate side-chains
  107 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
** A 568 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 = 0.3999 r_free = 0.3999 target = 0.131902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.100950 restraints weight = 13914.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.104378 restraints weight = 6995.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.106629 restraints weight = 4532.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.8255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5645  Z= 0.169
  Angle     :  0.739  10.083   7669  Z= 0.361
  Chirality :  0.045   0.246    875
  Planarity :  0.004   0.034    941
  Dihedral  :  4.314  16.886    729
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 24.18 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.34), residues: 671
  helix:  1.22 (0.26), residues: 410
  sheet: -0.87 (1.57), residues: 12
  loop : -1.95 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 116 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.046   0.002   PHE A 529 
 TYR   0.029   0.002   TYR A 559 
 ARG   0.008   0.001   ARG A 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04451 (  301)
  hydrogen bonds       : angle       4.16593 (  891)
  SS BOND              : bond        0.00089 (    2)
  SS BOND              : angle       0.35937 (    4)
  covalent geometry    : bond        0.00390 ( 5643)
  covalent geometry    : angle       0.73959 ( 7665)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7001 (t80)
REVERT: A  496 SER cc_start: 0.9000 (m) cc_final: 0.8611 (p)
REVERT: A  585 MET cc_start: 0.1598 (tmm) cc_final: 0.0066 (mmt)
REVERT: A  668 VAL cc_start: 0.8417 (t) cc_final: 0.8131 (p)
REVERT: A  670 GLN cc_start: 0.8791 (tt0) cc_final: 0.8534 (tp-100)
  outliers start: 25
  outliers final: 22
  residues processed: 101
  average time/residue: 0.1219
  time to fit residues: 17.7645
Evaluate side-chains
  95 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 0 optimal weight:   10.9990
   chunk 9 optimal weight:    0.1980
   chunk 40 optimal weight:    0.0970
   chunk 43 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 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 = 0.135097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.105272 restraints weight = 13740.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.108920 restraints weight = 6746.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.111356 restraints weight = 4278.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
moved from start:          0.8327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5645  Z= 0.123
  Angle     :  0.718  12.043   7669  Z= 0.339
  Chirality :  0.042   0.233    875
  Planarity :  0.004   0.034    941
  Dihedral  :  4.114  17.177    729
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 26.97 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.34), residues: 671
  helix:  1.23 (0.27), residues: 416
  sheet: -1.05 (1.50), residues: 12
  loop : -1.94 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 531 
 HIS   0.002   0.001   HIS A 196 
 PHE   0.050   0.001   PHE A 529 
 TYR   0.027   0.002   TYR A  33 
 ARG   0.002   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  301)
  hydrogen bonds       : angle       4.01146 (  891)
  SS BOND              : bond        0.00043 (    2)
  SS BOND              : angle       0.42211 (    4)
  covalent geometry    : bond        0.00270 ( 5643)
  covalent geometry    : angle       0.71837 ( 7665)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2027.13 seconds
wall clock time: 36 minutes 12.21 seconds (2172.21 seconds total)