Starting phenix.real_space_refine
on Fri Oct 10 12:57:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wua_37852/10_2025/8wua_37852.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wua_37852/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wua_37852/10_2025/8wua_37852.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wua_37852/10_2025/8wua_37852.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wua_37852/10_2025/8wua_37852.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wua_37852/10_2025/8wua_37852.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.30
  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: 0.45
  Conformation dependent library (CDL) restraints added in 205.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.13
  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: 0.63

  Time building geometry restraints manager: 0.62 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:             1.500
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.150
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.120
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 296 
 TYR   0.014   0.001   TYR A 203 
 PHE   0.045   0.001   PHE A 529 
 TRP   0.007   0.001   TRP A 131 
 HIS   0.003   0.001   HIS A 648 

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

*********************** 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  : 0.225 
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: 0.0594
  time to fit residues: 6.6794
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  : 0.214 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4455 r_free = 0.4455 target = 0.167557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.139566 restraints weight = 14848.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.143532 restraints weight = 7757.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.146066 restraints weight = 5081.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.147726 restraints weight = 3859.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.148651 restraints weight = 3242.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.4220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5645  Z= 0.135
  Angle     :  0.626  10.992   7669  Z= 0.303
  Chirality :  0.041   0.147    875
  Planarity :  0.004   0.047    941
  Dihedral  :  4.500  46.761    733
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 19.24 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.34), residues: 671
  helix:  1.26 (0.27), residues: 408
  sheet:  0.16 (1.43), residues: 17
  loop : -2.04 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 228 
 TYR   0.017   0.002   TYR A 323 
 PHE   0.032   0.001   PHE A 529 
 TRP   0.020   0.001   TRP A 395 
 HIS   0.007   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5643)
  covalent geometry    : angle       0.62547 ( 7665)
  SS BOND              : bond        0.00095 (    2)
  SS BOND              : angle       0.72820 (    4)
  hydrogen bonds       : bond        0.03503 (  301)
  hydrogen bonds       : angle       3.90734 (  891)

*********************** 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
  126 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4700 (ptm160) cc_final: 0.4069 (tpt170)
REVERT: A  265 ASN cc_start: 0.8337 (t0) cc_final: 0.8093 (t0)
REVERT: A  327 MET cc_start: 0.6945 (mpp) cc_final: 0.6509 (ptp)
REVERT: A  437 THR cc_start: 0.6443 (m) cc_final: 0.6207 (t)
REVERT: A  545 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8109 (tm-30)
REVERT: A  683 TYR cc_start: 0.7429 (t80) cc_final: 0.7221 (t80)
  outliers start: 27
  outliers final: 14
  residues processed: 116
  average time/residue: 0.0559
  time to fit residues: 9.2633
Evaluate side-chains
  104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  435 PHE
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  522 LEU
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  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 3 optimal weight:    0.0970
   chunk 55 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 25 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 643 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.162575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.134138 restraints weight = 14841.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.138023 restraints weight = 7856.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.140451 restraints weight = 5192.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.142115 restraints weight = 3965.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.143143 restraints weight = 3328.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5645  Z= 0.108
  Angle     :  0.574  10.508   7669  Z= 0.274
  Chirality :  0.040   0.170    875
  Planarity :  0.003   0.035    941
  Dihedral  :  3.838  35.824    731
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 21.88 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.34), residues: 671
  helix:  1.44 (0.27), residues: 408
  sheet: -0.13 (1.43), residues: 17
  loop : -2.06 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 228 
 TYR   0.012   0.001   TYR A 203 
 PHE   0.035   0.001   PHE A 529 
 TRP   0.010   0.001   TRP A 131 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 5643)
  covalent geometry    : angle       0.57416 ( 7665)
  SS BOND              : bond        0.00291 (    2)
  SS BOND              : angle       0.54077 (    4)
  hydrogen bonds       : bond        0.03148 (  301)
  hydrogen bonds       : angle       3.71793 (  891)

*********************** 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
  113 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7220 (m-80) cc_final: 0.6951 (m-80)
REVERT: A  265 ASN cc_start: 0.8516 (t0) cc_final: 0.8277 (t0)
REVERT: A  270 ILE cc_start: 0.7902 (mm) cc_final: 0.7571 (mm)
REVERT: A  409 LYS cc_start: 0.8083 (pttt) cc_final: 0.7753 (pttp)
REVERT: A  413 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6927 (pt)
REVERT: A  513 MET cc_start: 0.8492 (tmm) cc_final: 0.7739 (tmm)
REVERT: A  627 THR cc_start: 0.7665 (m) cc_final: 0.7107 (p)
REVERT: A  683 TYR cc_start: 0.7434 (t80) cc_final: 0.7017 (t80)
  outliers start: 20
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0560
  time to fit residues: 8.4262
Evaluate side-chains
  101 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  162 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  413 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  435 PHE
Chi-restraints excluded: chain A residue  508 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0370
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
A 265 ASN
A 604 GLN
A 664 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.148220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.117902 restraints weight = 13879.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.121836 restraints weight = 7254.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.124358 restraints weight = 4724.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.125964 restraints weight = 3557.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.126987 restraints weight = 2972.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.4687

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= 0.129
  Angle     :  0.600  10.253   7669  Z= 0.289
  Chirality :  0.041   0.151    875
  Planarity :  0.003   0.035    941
  Dihedral  :  3.681  17.876    729
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 20.39 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.34), residues: 671
  helix:  1.49 (0.27), residues: 410
  sheet: -0.43 (1.39), residues: 17
  loop : -1.95 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  74 
 TYR   0.014   0.001   TYR A 323 
 PHE   0.039   0.001   PHE A 529 
 TRP   0.011   0.001   TRP A 131 
 HIS   0.006   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5643)
  covalent geometry    : angle       0.59993 ( 7665)
  SS BOND              : bond        0.00036 (    2)
  SS BOND              : angle       0.24280 (    4)
  hydrogen bonds       : bond        0.03662 (  301)
  hydrogen bonds       : angle       3.82818 (  891)

*********************** 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
  131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7251 (m-80) cc_final: 0.6765 (m-10)
REVERT: A   74 ARG cc_start: 0.4579 (ptm160) cc_final: 0.3972 (tpt170)
REVERT: A  270 ILE cc_start: 0.8348 (mm) cc_final: 0.8058 (mm)
REVERT: A  413 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7456 (pt)
REVERT: A  449 PHE cc_start: 0.8029 (m-80) cc_final: 0.7542 (m-80)
REVERT: A  544 LEU cc_start: 0.8274 (pt) cc_final: 0.7807 (pp)
REVERT: A  545 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8092 (pp20)
  outliers start: 36
  outliers final: 22
  residues processed: 115
  average time/residue: 0.0507
  time to fit residues: 8.5239
Evaluate side-chains
  108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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  129 LEU
Chi-restraints excluded: chain A residue  137 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  470 LEU
Chi-restraints excluded: chain A residue  545 GLU
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  702 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0980
   chunk 60 optimal weight:    0.6980
   chunk 63 optimal weight:    0.2980
   chunk 29 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
** A 265 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 = 0.4193 r_free = 0.4193 target = 0.147471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.117214 restraints weight = 13986.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.121175 restraints weight = 7136.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.123673 restraints weight = 4586.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.125317 restraints weight = 3451.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.126364 restraints weight = 2873.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5645  Z= 0.106
  Angle     :  0.588   9.858   7669  Z= 0.279
  Chirality :  0.040   0.220    875
  Planarity :  0.003   0.035    941
  Dihedral  :  3.539  18.178    729
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.51 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.34), residues: 671
  helix:  1.58 (0.27), residues: 408
  sheet: -0.35 (1.38), residues: 17
  loop : -1.94 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 326 
 TYR   0.017   0.001   TYR A 683 
 PHE   0.043   0.001   PHE A 529 
 TRP   0.011   0.001   TRP A 131 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 5643)
  covalent geometry    : angle       0.58859 ( 7665)
  SS BOND              : bond        0.00026 (    2)
  SS BOND              : angle       0.33304 (    4)
  hydrogen bonds       : bond        0.03205 (  301)
  hydrogen bonds       : angle       3.66071 (  891)

*********************** 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
  112 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   31 TYR cc_start: 0.7212 (m-80) cc_final: 0.6800 (m-10)
REVERT: A   74 ARG cc_start: 0.4594 (ptm160) cc_final: 0.4088 (tpt170)
REVERT: A  270 ILE cc_start: 0.8255 (mm) cc_final: 0.7933 (mm)
REVERT: A  413 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7349 (pt)
REVERT: A  627 THR cc_start: 0.7822 (m) cc_final: 0.7187 (p)
  outliers start: 24
  outliers final: 19
  residues processed: 100
  average time/residue: 0.0507
  time to fit residues: 7.4756
Evaluate side-chains
  105 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  156 LEU
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  413 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  435 PHE
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  702 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5356

-------------------------------------------------------------------------------
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 = 0.4163 r_free = 0.4163 target = 0.145319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.115305 restraints weight = 13724.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.119171 restraints weight = 6978.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.121669 restraints weight = 4487.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.123300 restraints weight = 3361.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.124356 restraints weight = 2794.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6566
moved from start:          0.5495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5645  Z= 0.107
  Angle     :  0.597   9.735   7669  Z= 0.281
  Chirality :  0.040   0.180    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.498  17.859    729
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 23.68 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.34), residues: 671
  helix:  1.59 (0.27), residues: 409
  sheet: -0.31 (1.34), residues: 17
  loop : -1.98 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 326 
 TYR   0.012   0.001   TYR A 203 
 PHE   0.042   0.001   PHE A 529 
 TRP   0.012   0.001   TRP A 131 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 5643)
  covalent geometry    : angle       0.59663 ( 7665)
  SS BOND              : bond        0.00068 (    2)
  SS BOND              : angle       0.47449 (    4)
  hydrogen bonds       : bond        0.03253 (  301)
  hydrogen bonds       : angle       3.65641 (  891)

*********************** 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
  118 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7338 (m-80) cc_final: 0.6807 (m-10)
REVERT: A   74 ARG cc_start: 0.4606 (ptm160) cc_final: 0.4108 (tpt170)
REVERT: A  268 LYS cc_start: 0.8845 (tppt) cc_final: 0.8629 (tptp)
REVERT: A  270 ILE cc_start: 0.8289 (mm) cc_final: 0.7962 (mm)
REVERT: A  413 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7502 (pt)
REVERT: A  427 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.6954 (t80)
REVERT: A  544 LEU cc_start: 0.8259 (pt) cc_final: 0.7892 (pp)
REVERT: A  683 TYR cc_start: 0.8099 (t80) cc_final: 0.7450 (t80)
  outliers start: 27
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0562
  time to fit residues: 8.6048
Evaluate side-chains
  113 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  129 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  156 LEU
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  423 LEU
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
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  702 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 27 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.134705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.103868 restraints weight = 14024.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.107452 restraints weight = 7092.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.109734 restraints weight = 4597.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.111292 restraints weight = 3477.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.112044 restraints weight = 2904.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.7243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5645  Z= 0.164
  Angle     :  0.691  10.733   7669  Z= 0.333
  Chirality :  0.044   0.191    875
  Planarity :  0.004   0.037    941
  Dihedral  :  4.119  18.209    729
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 24.18 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.34), residues: 671
  helix:  1.45 (0.27), residues: 405
  sheet: -0.53 (1.25), residues: 17
  loop : -2.07 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  72 
 TYR   0.012   0.001   TYR A 624 
 PHE   0.050   0.002   PHE A 529 
 TRP   0.016   0.001   TRP A 531 
 HIS   0.006   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 5643)
  covalent geometry    : angle       0.69139 ( 7665)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.33748 (    4)
  hydrogen bonds       : bond        0.04362 (  301)
  hydrogen bonds       : angle       3.97038 (  891)

*********************** 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
  119 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   31 TYR cc_start: 0.7631 (m-80) cc_final: 0.7063 (m-80)
REVERT: A  266 VAL cc_start: 0.9054 (m) cc_final: 0.8698 (p)
REVERT: A  270 ILE cc_start: 0.8523 (mm) cc_final: 0.8151 (mm)
REVERT: A  427 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7047 (t80)
REVERT: A  496 SER cc_start: 0.9122 (m) cc_final: 0.8723 (p)
REVERT: A  559 TYR cc_start: 0.8309 (t80) cc_final: 0.8083 (t80)
  outliers start: 26
  outliers final: 19
  residues processed: 109
  average time/residue: 0.0485
  time to fit residues: 7.7558
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  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  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  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 22 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0770
   chunk 51 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.137328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.106657 restraints weight = 13882.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.110340 restraints weight = 6954.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.112745 restraints weight = 4474.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.114313 restraints weight = 3364.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.115200 restraints weight = 2800.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.7490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5645  Z= 0.120
  Angle     :  0.654  10.127   7669  Z= 0.314
  Chirality :  0.042   0.191    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.824  17.145    729
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 25.16 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.34), residues: 671
  helix:  1.46 (0.26), residues: 411
  sheet: -0.35 (1.31), residues: 17
  loop : -2.08 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 530 
 TYR   0.013   0.001   TYR A 362 
 PHE   0.045   0.001   PHE A 529 
 TRP   0.014   0.001   TRP A 473 
 HIS   0.002   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5643)
  covalent geometry    : angle       0.65383 ( 7665)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.36545 (    4)
  hydrogen bonds       : bond        0.03616 (  301)
  hydrogen bonds       : angle       3.79432 (  891)

*********************** 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
  117 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7462 (m-80) cc_final: 0.6779 (m-80)
REVERT: A  266 VAL cc_start: 0.9010 (m) cc_final: 0.8774 (p)
REVERT: A  380 GLU cc_start: 0.8420 (pm20) cc_final: 0.7966 (mp0)
REVERT: A  427 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7031 (t80)
REVERT: A  496 SER cc_start: 0.9121 (m) cc_final: 0.8691 (p)
REVERT: A  531 TRP cc_start: 0.7083 (t-100) cc_final: 0.6865 (t-100)
REVERT: A  585 MET cc_start: 0.1997 (tmm) cc_final: 0.0358 (mmt)
  outliers start: 27
  outliers final: 22
  residues processed: 105
  average time/residue: 0.0477
  time to fit residues: 7.5703
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  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  137 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  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  435 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  679 LEU
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 20 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0670
   chunk 48 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0670
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0060
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    0.2980
   chunk 30 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0770
   overall best weight:    0.1030

-------------------------------------------------------------------------------
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 = 0.4123 r_free = 0.4123 target = 0.141524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.111333 restraints weight = 13763.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.115249 restraints weight = 6792.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.117771 restraints weight = 4291.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.119409 restraints weight = 3189.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.120293 restraints weight = 2629.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
moved from start:          0.7395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5645  Z= 0.112
  Angle     :  0.671  10.340   7669  Z= 0.313
  Chirality :  0.041   0.211    875
  Planarity :  0.003   0.033    941
  Dihedral  :  3.685  18.032    729
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 27.30 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.34), residues: 671
  helix:  1.56 (0.27), residues: 403
  sheet: -0.24 (1.26), residues: 17
  loop : -1.82 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 296 
 TYR   0.016   0.001   TYR A 559 
 PHE   0.043   0.001   PHE A 529 
 TRP   0.016   0.001   TRP A 473 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5643)
  covalent geometry    : angle       0.67069 ( 7665)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.69040 (    4)
  hydrogen bonds       : bond        0.03226 (  301)
  hydrogen bonds       : angle       3.71831 (  891)

*********************** 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
  115 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7220 (m-80) cc_final: 0.6762 (m-80)
REVERT: A  380 GLU cc_start: 0.8360 (pm20) cc_final: 0.7789 (mp0)
REVERT: A  427 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7092 (t80)
REVERT: A  436 LEU cc_start: 0.6722 (tt) cc_final: 0.6465 (tt)
REVERT: A  496 SER cc_start: 0.8928 (m) cc_final: 0.8501 (p)
REVERT: A  585 MET cc_start: 0.1965 (tmm) cc_final: 0.0440 (mmm)
REVERT: A  627 THR cc_start: 0.7601 (m) cc_final: 0.7025 (p)
  outliers start: 19
  outliers final: 18
  residues processed: 109
  average time/residue: 0.0527
  time to fit residues: 8.2700
Evaluate side-chains
  109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
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  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  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  672 LEU
Chi-restraints excluded: chain A residue  679 LEU
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 34 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0670
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0060
   chunk 3 optimal weight:    0.0670
   chunk 36 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.3672

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.140381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.110482 restraints weight = 14095.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.114282 restraints weight = 6951.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.116801 restraints weight = 4397.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.118447 restraints weight = 3265.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.119510 restraints weight = 2690.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.7578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5645  Z= 0.113
  Angle     :  0.667  10.509   7669  Z= 0.312
  Chirality :  0.042   0.198    875
  Planarity :  0.004   0.053    941
  Dihedral  :  3.622  17.143    729
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 27.47 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.34), residues: 671
  helix:  1.59 (0.27), residues: 409
  sheet: -0.28 (1.21), residues: 17
  loop : -1.88 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 296 
 TYR   0.020   0.001   TYR A 559 
 PHE   0.048   0.001   PHE A 529 
 TRP   0.024   0.001   TRP A 531 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5643)
  covalent geometry    : angle       0.66723 ( 7665)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       0.36507 (    4)
  hydrogen bonds       : bond        0.03349 (  301)
  hydrogen bonds       : angle       3.75354 (  891)

********************** 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
  105 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7223 (m-80) cc_final: 0.6692 (m-80)
REVERT: A  380 GLU cc_start: 0.8325 (pm20) cc_final: 0.7855 (pm20)
REVERT: A  496 SER cc_start: 0.8921 (m) cc_final: 0.8497 (p)
REVERT: A  515 LEU cc_start: 0.7584 (tt) cc_final: 0.7350 (tt)
REVERT: A  585 MET cc_start: 0.2162 (tmm) cc_final: 0.0616 (mmm)
REVERT: A  627 THR cc_start: 0.7663 (m) cc_final: 0.7116 (p)
  outliers start: 16
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0422
  time to fit residues: 6.3607
Evaluate side-chains
  103 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
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  367 PHE
Chi-restraints excluded: chain A residue  470 LEU
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  679 LEU
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 64 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 14 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 343 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.136205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.106210 restraints weight = 14136.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.109956 restraints weight = 6952.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.112375 restraints weight = 4382.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.113935 restraints weight = 3261.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.114866 restraints weight = 2698.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.8237

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= 0.130
  Angle     :  0.682  10.033   7669  Z= 0.323
  Chirality :  0.043   0.200    875
  Planarity :  0.004   0.039    941
  Dihedral  :  3.790  17.794    729
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 26.81 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.34), residues: 671
  helix:  1.68 (0.27), residues: 403
  sheet: -0.34 (1.23), residues: 17
  loop : -1.91 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  74 
 TYR   0.021   0.001   TYR A 559 
 PHE   0.049   0.001   PHE A 529 
 TRP   0.018   0.001   TRP A 531 
 HIS   0.003   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5643)
  covalent geometry    : angle       0.68201 ( 7665)
  SS BOND              : bond        0.00011 (    2)
  SS BOND              : angle       0.16847 (    4)
  hydrogen bonds       : bond        0.03738 (  301)
  hydrogen bonds       : angle       3.82289 (  891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1146.06 seconds
wall clock time: 20 minutes 24.82 seconds (1224.82 seconds total)