Starting phenix.real_space_refine
on Sun Apr 27 11:20:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wua_37852/04_2025/8wua_37852.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wua_37852/04_2025/8wua_37852.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wua_37852/04_2025/8wua_37852.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wua_37852/04_2025/8wua_37852.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wua_37852/04_2025/8wua_37852.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wua_37852/04_2025/8wua_37852.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    3622      2.51       5
     N     888      2.21       5
     O     946      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5494
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 5494
          Classifications: {'peptide': 675}
          Link IDs: {'PTRANS': 26, 'TRANS': 648}
          Chain breaks: 1
  Time building chain proxies: 4.03, per 1000 atoms: 0.73
  Number of scatterers: 5494
  At special positions: 0
  Unit cell: (91.1257, 96.6152, 92.2236, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O     946      8.00
     N     888      7.00
     C    3622      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 639.5 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 2 sheets defined
      65.2% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 18
      removed outlier: 4.130A  pdb=" N   ARG A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 21
      No H-bonds generated for 'chain 'A' and resid 19 through 21'
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 49 through 75
      removed outlier: 3.712A  pdb=" N   VAL A  53 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 123
      removed outlier: 4.001A  pdb=" N   ILE A 120 " --> pdb=" O   TRP A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 132
    Processing helix  chain 'A' and resid 134 through 158
      removed outlier: 3.791A  pdb=" N   HIS A 138 " --> pdb=" O   GLU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 167
      removed outlier: 3.822A  pdb=" N   VAL A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 182
      removed outlier: 3.749A  pdb=" N   THR A 181 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 219
      removed outlier: 3.793A  pdb=" N   HIS A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LEU A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 205 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 252
    Processing helix  chain 'A' and resid 266 through 294
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 4.116A  pdb=" N   PHE A 307 " --> pdb=" O   CYS A 304 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   CYS A 308 " --> pdb=" O   GLY A 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 308'
    Processing helix  chain 'A' and resid 320 through 341
      removed outlier: 3.651A  pdb=" N   ARG A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 345
      removed outlier: 3.753A  pdb=" N   GLN A 345 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 342 through 345'
    Processing helix  chain 'A' and resid 357 through 365
    Processing helix  chain 'A' and resid 415 through 445
      removed outlier: 3.915A  pdb=" N   TRP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   THR A 428 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 466 through 491
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 494 through 515
      removed outlier: 4.153A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   GLN A 500 " --> pdb=" O   SER A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 534
    Processing helix  chain 'A' and resid 550 through 553
    Processing helix  chain 'A' and resid 554 through 565
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 574 through 587
    Processing helix  chain 'A' and resid 594 through 599
      removed outlier: 3.767A  pdb=" N   LYS A 598 " --> pdb=" O   ARG A 594 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN A 599 " --> pdb=" O   ARG A 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 594 through 599'
    Processing helix  chain 'A' and resid 606 through 624
    Processing helix  chain 'A' and resid 630 through 650
      removed outlier: 3.984A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 673
      removed outlier: 3.598A  pdb=" N   ALA A 673 " --> pdb=" O   ASN A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 690
    Processing helix  chain 'A' and resid 694 through 710
      removed outlier: 3.588A  pdb=" N   LEU A 698 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 717
      removed outlier: 4.042A  pdb=" N   PHE A 717 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 262
      removed outlier: 3.814A  pdb=" N   ILE A 232 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL A 352 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   THR A 396 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299

    301 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.55 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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.970
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5848
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.162   5645  Z= 0.137
  Angle     :  0.750  16.137   7669  Z= 0.376
  Chirality :  0.041   0.286    875
  Planarity :  0.006   0.114    941
  Dihedral  : 15.346  89.998   2015
  Min Nonbonded Distance : 2.105

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

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

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

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

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.660 
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: 0.1438
  time to fit residues: 15.8002
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  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   overall best weight:    0.5996

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.170671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.144028 restraints weight = 14621.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.147886 restraints weight = 7836.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.150366 restraints weight = 5180.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.2085

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

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

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

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

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

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.4858 (ptm160) cc_final: 0.4151 (tpt170)
REVERT: A  265 ASN cc_start: 0.8291 (t0) cc_final: 0.7978 (t0)
REVERT: A  327 MET cc_start: 0.6844 (mpp) cc_final: 0.6543 (ptp)
REVERT: A  413 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6833 (pt)
REVERT: A  437 THR cc_start: 0.6427 (m) cc_final: 0.6219 (t)
REVERT: A  614 MET cc_start: 0.7904 (ttm) cc_final: 0.7685 (ttm)
REVERT: A  627 THR cc_start: 0.7980 (m) cc_final: 0.7432 (p)
REVERT: A  683 TYR cc_start: 0.7193 (t80) cc_final: 0.6981 (t80)
  outliers start: 24
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1227
  time to fit residues: 17.7628
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  435 PHE
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A 604 GLN
** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.153531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.123634 restraints weight = 14517.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.127384 restraints weight = 7685.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.129712 restraints weight = 5098.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.4519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5645  Z= 0.147
  Angle     :  0.662  10.531   7669  Z= 0.318
  Chirality :  0.042   0.159    875
  Planarity :  0.004   0.036    941
  Dihedral  :  4.185  35.758    731
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 20.72 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.34), residues: 671
  helix:  1.33 (0.27), residues: 409
  sheet: -0.22 (1.40), residues: 17
  loop : -2.06 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 395 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.032   0.001   PHE A 529 
 TYR   0.013   0.001   TYR A 362 
 ARG   0.005   0.001   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04081 (  301)
  hydrogen bonds       : angle       3.86478 (  891)
  SS BOND              : bond        0.00038 (    2)
  SS BOND              : angle       0.22742 (    4)
  covalent geometry    : bond        0.00326 ( 5643)
  covalent geometry    : angle       0.66229 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.4495 (ptm160) cc_final: 0.3915 (tpt170)
REVERT: A  265 ASN cc_start: 0.8823 (t0) cc_final: 0.8604 (t0)
REVERT: A  270 ILE cc_start: 0.7927 (mm) cc_final: 0.7621 (mm)
REVERT: A  327 MET cc_start: 0.7169 (mpp) cc_final: 0.6876 (ptp)
REVERT: A  449 PHE cc_start: 0.8034 (m-80) cc_final: 0.7526 (m-80)
REVERT: A  544 LEU cc_start: 0.8217 (pt) cc_final: 0.7712 (pp)
REVERT: A  545 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8263 (pp20)
REVERT: A  683 TYR cc_start: 0.7865 (t80) cc_final: 0.7371 (t80)
  outliers start: 31
  outliers final: 15
  residues processed: 124
  average time/residue: 0.1273
  time to fit residues: 22.3151
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  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  545 GLU
Chi-restraints excluded: chain A residue  566 ILE
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  682 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 27 optimal weight:    8.9990
   chunk 47 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 HIS
A 670 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.145310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.114241 restraints weight = 14176.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.118141 restraints weight = 7265.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.120674 restraints weight = 4703.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.5293

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= 0.122
  Angle     :  0.619  13.692   7669  Z= 0.294
  Chirality :  0.041   0.138    875
  Planarity :  0.003   0.036    941
  Dihedral  :  3.794  16.803    729
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 22.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.34), residues: 671
  helix:  1.46 (0.27), residues: 410
  sheet: -0.51 (1.32), residues: 17
  loop : -2.02 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 473 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.037   0.001   PHE A 529 
 TYR   0.016   0.001   TYR A 559 
 ARG   0.005   0.000   ARG A 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03534 (  301)
  hydrogen bonds       : angle       3.67267 (  891)
  SS BOND              : bond        0.00169 (    2)
  SS BOND              : angle       0.55767 (    4)
  covalent geometry    : bond        0.00271 ( 5643)
  covalent geometry    : angle       0.61864 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A   31 TYR cc_start: 0.7185 (m-80) cc_final: 0.6948 (m-80)
REVERT: A   74 ARG cc_start: 0.4545 (ptm160) cc_final: 0.3899 (tpt170)
REVERT: A  270 ILE cc_start: 0.8283 (mm) cc_final: 0.7966 (mm)
REVERT: A  544 LEU cc_start: 0.8378 (pt) cc_final: 0.7910 (pp)
REVERT: A  670 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8262 (tm130)
  outliers start: 25
  outliers final: 16
  residues processed: 105
  average time/residue: 0.1144
  time to fit residues: 17.3709
Evaluate side-chains
  102 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  435 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  670 GLN
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0770
   chunk 41 optimal weight:    0.0040
   chunk 52 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.5150

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.144778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.114482 restraints weight = 13716.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.118353 restraints weight = 7041.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.120849 restraints weight = 4548.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.5563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5645  Z= 0.112
  Angle     :  0.617  10.002   7669  Z= 0.294
  Chirality :  0.040   0.183    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.722  18.104    729
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.36 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.34), residues: 671
  helix:  1.53 (0.27), residues: 410
  sheet: -0.25 (1.41), residues: 16
  loop : -2.00 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 131 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.044   0.001   PHE A 529 
 TYR   0.013   0.001   TYR A 323 
 ARG   0.001   0.000   ARG A 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03404 (  301)
  hydrogen bonds       : angle       3.59699 (  891)
  SS BOND              : bond        0.00062 (    2)
  SS BOND              : angle       0.44068 (    4)
  covalent geometry    : bond        0.00241 ( 5643)
  covalent geometry    : angle       0.61725 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A   31 TYR cc_start: 0.7189 (m-80) cc_final: 0.6822 (m-80)
REVERT: A   74 ARG cc_start: 0.4554 (ptm160) cc_final: 0.3922 (tpt170)
REVERT: A  270 ILE cc_start: 0.8372 (mm) cc_final: 0.8043 (mm)
REVERT: A  427 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7024 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1214
  time to fit residues: 18.0344
Evaluate side-chains
  101 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 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  427 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  620 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0980
   chunk 30 optimal weight:    4.9990
   chunk 57 optimal weight:    0.1980
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6382

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.142352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.112122 restraints weight = 13568.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.115875 restraints weight = 6873.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.118347 restraints weight = 4440.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
moved from start:          0.6082

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= 0.114
  Angle     :  0.618  10.011   7669  Z= 0.295
  Chirality :  0.041   0.179    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.667  16.922    729
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 23.03 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.34), residues: 671
  helix:  1.56 (0.27), residues: 412
  sheet: -0.57 (1.35), residues: 16
  loop : -2.03 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 473 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.043   0.001   PHE A 529 
 TYR   0.016   0.001   TYR A 559 
 ARG   0.001   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03365 (  301)
  hydrogen bonds       : angle       3.62794 (  891)
  SS BOND              : bond        0.00047 (    2)
  SS BOND              : angle       0.37556 (    4)
  covalent geometry    : bond        0.00248 ( 5643)
  covalent geometry    : angle       0.61804 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7286 (m-80) cc_final: 0.6871 (m-80)
REVERT: A   74 ARG cc_start: 0.4471 (ptm160) cc_final: 0.3883 (tpt170)
REVERT: A  270 ILE cc_start: 0.8418 (mm) cc_final: 0.8101 (mm)
REVERT: A  427 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7022 (t80)
REVERT: A  683 TYR cc_start: 0.8112 (t80) cc_final: 0.7153 (t80)
  outliers start: 26
  outliers final: 19
  residues processed: 107
  average time/residue: 0.1326
  time to fit residues: 19.8921
Evaluate side-chains
  106 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
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  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  535 LYS
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   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 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 = 0.4094 r_free = 0.4094 target = 0.139327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.108977 restraints weight = 13607.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.112705 restraints weight = 6880.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.115105 restraints weight = 4424.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6716
moved from start:          0.6707

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= 0.122
  Angle     :  0.624   9.790   7669  Z= 0.297
  Chirality :  0.041   0.156    875
  Planarity :  0.003   0.034    941
  Dihedral  :  3.729  17.976    729
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.36 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.34), residues: 671
  helix:  1.58 (0.27), residues: 412
  sheet: -0.39 (1.36), residues: 16
  loop : -2.00 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 473 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.044   0.001   PHE A 529 
 TYR   0.019   0.001   TYR A 559 
 ARG   0.002   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  301)
  hydrogen bonds       : angle       3.61024 (  891)
  SS BOND              : bond        0.00018 (    2)
  SS BOND              : angle       0.37327 (    4)
  covalent geometry    : bond        0.00275 ( 5643)
  covalent geometry    : angle       0.62454 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.591 
Fit side-chains
REVERT: A   31 TYR cc_start: 0.7315 (m-80) cc_final: 0.6904 (m-80)
REVERT: A   74 ARG cc_start: 0.4178 (ptm160) cc_final: 0.3849 (tpt170)
REVERT: A  270 ILE cc_start: 0.8446 (mm) cc_final: 0.8141 (mm)
REVERT: A  427 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.6936 (t80)
REVERT: A  496 SER cc_start: 0.8919 (m) cc_final: 0.8530 (p)
REVERT: A  683 TYR cc_start: 0.8378 (t80) cc_final: 0.7132 (t80)
  outliers start: 30
  outliers final: 19
  residues processed: 111
  average time/residue: 0.1213
  time to fit residues: 19.2558
Evaluate side-chains
  101 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
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   50 ILE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 30 optimal weight:    0.0170
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0470
   chunk 63 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.5116

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.139935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.109925 restraints weight = 13717.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.113675 restraints weight = 6915.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.116113 restraints weight = 4451.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6732
moved from start:          0.6974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5645  Z= 0.113
  Angle     :  0.646   9.961   7669  Z= 0.308
  Chirality :  0.041   0.178    875
  Planarity :  0.003   0.033    941
  Dihedral  :  3.760  16.757    729
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.34 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.35), residues: 671
  helix:  1.60 (0.27), residues: 412
  sheet: -0.44 (1.38), residues: 16
  loop : -1.97 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 531 
 HIS   0.004   0.001   HIS A 196 
 PHE   0.042   0.001   PHE A 529 
 TYR   0.028   0.001   TYR A 683 
 ARG   0.001   0.000   ARG A 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  301)
  hydrogen bonds       : angle       3.65952 (  891)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       0.38214 (    4)
  covalent geometry    : bond        0.00246 ( 5643)
  covalent geometry    : angle       0.64566 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A   31 TYR cc_start: 0.7234 (m-80) cc_final: 0.6833 (m-10)
REVERT: A   74 ARG cc_start: 0.4190 (ptm160) cc_final: 0.3883 (tpt170)
REVERT: A  270 ILE cc_start: 0.8437 (mm) cc_final: 0.8122 (mm)
REVERT: A  327 MET cc_start: 0.7425 (ptp) cc_final: 0.7165 (pmm)
REVERT: A  427 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.6928 (t80)
REVERT: A  496 SER cc_start: 0.8895 (m) cc_final: 0.8503 (p)
REVERT: A  708 ILE cc_start: 0.8895 (mm) cc_final: 0.8678 (pt)
  outliers start: 24
  outliers final: 21
  residues processed: 102
  average time/residue: 0.1846
  time to fit residues: 28.4223
Evaluate side-chains
  105 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 46 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0270
   overall best weight:    0.6040

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.137899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.107783 restraints weight = 13908.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.111383 restraints weight = 6952.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.113817 restraints weight = 4460.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.7446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5645  Z= 0.115
  Angle     :  0.642  10.294   7669  Z= 0.305
  Chirality :  0.041   0.170    875
  Planarity :  0.003   0.033    941
  Dihedral  :  3.727  18.487    729
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 23.85 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.35), residues: 671
  helix:  1.66 (0.27), residues: 412
  sheet: -0.59 (1.36), residues: 16
  loop : -1.91 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 531 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.049   0.001   PHE A 529 
 TYR   0.018   0.001   TYR A 559 
 ARG   0.002   0.000   ARG A 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03391 (  301)
  hydrogen bonds       : angle       3.64151 (  891)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       0.19176 (    4)
  covalent geometry    : bond        0.00253 ( 5643)
  covalent geometry    : angle       0.64244 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A   31 TYR cc_start: 0.7288 (m-80) cc_final: 0.6944 (m-80)
REVERT: A   74 ARG cc_start: 0.4578 (ptm160) cc_final: 0.4282 (tpt170)
REVERT: A  270 ILE cc_start: 0.8519 (mm) cc_final: 0.8215 (mm)
REVERT: A  427 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7076 (t80)
REVERT: A  496 SER cc_start: 0.8893 (m) cc_final: 0.8485 (p)
REVERT: A  585 MET cc_start: 0.2021 (tmm) cc_final: 0.0530 (mmt)
REVERT: A  708 ILE cc_start: 0.8908 (mm) cc_final: 0.8701 (pt)
  outliers start: 25
  outliers final: 23
  residues processed: 103
  average time/residue: 0.1256
  time to fit residues: 18.8025
Evaluate side-chains
  106 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  522 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  620 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    0.1980
   chunk 25 optimal weight:    0.0570
   chunk 4 optimal weight:    0.0970
   chunk 55 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.2496

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.139965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.110237 restraints weight = 13750.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.114008 restraints weight = 6829.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.116431 restraints weight = 4338.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.7480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5645  Z= 0.110
  Angle     :  0.672  11.406   7669  Z= 0.316
  Chirality :  0.041   0.267    875
  Planarity :  0.003   0.033    941
  Dihedral  :  3.751  16.615    729
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 25.00 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.35), residues: 671
  helix:  1.66 (0.27), residues: 411
  sheet: -0.64 (1.32), residues: 16
  loop : -1.91 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 531 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.048   0.001   PHE A 529 
 TYR   0.023   0.001   TYR A 203 
 ARG   0.002   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  301)
  hydrogen bonds       : angle       3.72565 (  891)
  SS BOND              : bond        0.00061 (    2)
  SS BOND              : angle       0.33536 (    4)
  covalent geometry    : bond        0.00227 ( 5643)
  covalent geometry    : angle       0.67243 ( 7665)

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

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7174 (m-80) cc_final: 0.6871 (m-80)
REVERT: A  270 ILE cc_start: 0.8425 (mm) cc_final: 0.8106 (mm)
REVERT: A  427 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7202 (t80)
REVERT: A  496 SER cc_start: 0.8851 (m) cc_final: 0.8443 (p)
REVERT: A  585 MET cc_start: 0.2024 (tmm) cc_final: 0.0523 (mmm)
REVERT: A  708 ILE cc_start: 0.8934 (mm) cc_final: 0.8734 (pt)
  outliers start: 20
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1773
  time to fit residues: 25.2842
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  220 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  395 TRP
Chi-restraints excluded: chain A residue  427 PHE
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  702 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 9 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0030
   chunk 64 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.9194

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.136115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.105682 restraints weight = 14007.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.109370 restraints weight = 7061.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.111765 restraints weight = 4526.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6812
moved from start:          0.7959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5645  Z= 0.137
  Angle     :  0.733  19.526   7669  Z= 0.342
  Chirality :  0.043   0.227    875
  Planarity :  0.004   0.033    941
  Dihedral  :  3.912  17.569    729
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 25.00 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.35), residues: 671
  helix:  1.62 (0.27), residues: 412
  sheet: -1.40 (1.79), residues: 10
  loop : -1.88 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 531 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.048   0.001   PHE A 529 
 TYR   0.022   0.001   TYR A 559 
 ARG   0.004   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03817 (  301)
  hydrogen bonds       : angle       3.87155 (  891)
  SS BOND              : bond        0.00014 (    2)
  SS BOND              : angle       0.14009 (    4)
  covalent geometry    : bond        0.00316 ( 5643)
  covalent geometry    : angle       0.73269 ( 7665)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2195.30 seconds
wall clock time: 39 minutes 8.31 seconds (2348.31 seconds total)