Starting phenix.real_space_refine
on Sun Apr  5 01:21:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yjw_73037/04_2026/9yjw_73037.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yjw_73037/04_2026/9yjw_73037.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yjw_73037/04_2026/9yjw_73037.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yjw_73037/04_2026/9yjw_73037.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yjw_73037/04_2026/9yjw_73037.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yjw_73037/04_2026/9yjw_73037.map"
  }
  resolution = 4.2
  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=   0.001 sd=   0.019
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      15      5.16       5
     C    4130      2.51       5
     N    1196      2.21       5
     O    1268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6609
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6609
          Classifications: {'peptide': 842}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 24, 'TRANS': 817}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 1.48, per 1000 atoms: 0.22
  Number of scatterers: 6609
  At special positions: 0
  Unit cell: (99.96, 77.52, 134.64, 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      15     16.00
     O    1268      8.00
     N    1196      7.00
     C    4130      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 264 " - pdb=" SG  CYS A 272 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 446 " - pdb=" SG  CYS A 455 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 562 " - pdb=" SG  CYS A 572 " 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: 0.57
  Conformation dependent library (CDL) restraints added in 253.5 milliseconds
  

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1506

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 7 sheets defined
      7.1% alpha, 31.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 72
    Processing helix  chain 'A' and resid 75 through 81
      removed outlier: 3.607A  pdb=" N   LEU A  79 " --> pdb=" O   ASN A  75 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR A  80 " --> pdb=" O   ILE A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
      removed outlier: 3.910A  pdb=" N   VAL A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 350 through 362
    Processing helix  chain 'A' and resid 447 through 451
      removed outlier: 4.294A  pdb=" N   SER A 451 " --> pdb=" O   ALA A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 658
      removed outlier: 3.694A  pdb=" N   GLY A 658 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 882
      removed outlier: 3.531A  pdb=" N   VAL A 880 " --> pdb=" O   THR A 876 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 60 through 61
    current: chain 'A' and resid 116 through 117
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 116 through 117
    current: chain 'A' and resid 169 through 175
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90
      removed outlier: 4.829A  pdb=" N   GLY A  98 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 197
      removed outlier: 3.617A  pdb=" N   LYS A 193 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 305 through 314
    current: chain 'A' and resid 326 through 340
      removed outlier: 3.545A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 465 through 468
    current: chain 'A' and resid 494 through 513
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 494 through 513
    current: chain 'A' and resid 555 through 557
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 555 through 557
    current: chain 'A' and resid 596 through 602
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 596 through 602
    current: chain 'A' and resid 621 through 623
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 621 through 623
    current: chain 'A' and resid 640 through 649
      removed outlier: 3.955A  pdb=" N   ARG A 649 " --> pdb=" O   GLU A 673 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLU A 673 " --> pdb=" O   ARG A 649 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A 732 " --> pdb=" O   ASP A 768 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ASP A 768 " --> pdb=" O   ARG A 732 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   THR A 734 " --> pdb=" O   VAL A 766 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   VAL A 766 " --> pdb=" O   THR A 734 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   ILE A 736 " --> pdb=" O   MET A 764 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   MET A 764 " --> pdb=" O   ILE A 736 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   ILE A 738 " --> pdb=" O   ASN A 762 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   ASN A 762 " --> pdb=" O   ILE A 738 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLY A 740 " --> pdb=" O   ALA A 760 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   ALA A 760 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE A 742 " --> pdb=" O   THR A 758 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   THR A 758 " --> pdb=" O   ILE A 742 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN A 762 " --> pdb=" O   ARG A 790 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY A 805 " --> pdb=" O   TYR A 853 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR A 854 " --> pdb=" O   LEU A 862 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   THR A 861 " --> pdb=" O   GLU A 912 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 249
    Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 278
    Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 383
      removed outlier: 3.580A  pdb=" N   ALA A 387 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 724 through 727

    180 hydrogen bonds defined for protein.
    495 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: 1.13

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2228
        1.34 -     1.46: 1697
        1.46 -     1.58: 2811
        1.58 -     1.70: 0
        1.70 -     1.82: 24
  Bond restraints: 6760
  Sorted by residual:
  bond pdb=" CG  GLU A 717 "
       pdb=" CD  GLU A 717 "
    ideal  model  delta    sigma   weight residual
    1.516  1.471  0.045 2.50e-02 1.60e+03 3.17e+00
  bond pdb=" C   ASP A 777 "
       pdb=" N   ILE A 778 "
    ideal  model  delta    sigma   weight residual
    1.335  1.310  0.024 1.41e-02 5.03e+03 3.01e+00
  bond pdb=" CB  GLU A 717 "
       pdb=" CG  GLU A 717 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.81e+00
  bond pdb=" C   LYS A 633 "
       pdb=" N   PRO A 634 "
    ideal  model  delta    sigma   weight residual
    1.336  1.317  0.019 1.20e-02 6.94e+03 2.43e+00
  bond pdb=" C   LEU A 388 "
       pdb=" N   VAL A 389 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.46e-02 4.69e+03 1.60e+00
  ... (remaining 6755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 8840
        1.62 -     3.23: 264
        3.23 -     4.85: 27
        4.85 -     6.46: 6
        6.46 -     8.08: 2
  Bond angle restraints: 9139
  Sorted by residual:
  angle pdb=" N   GLY A 746 "
        pdb=" CA  GLY A 746 "
        pdb=" C   GLY A 746 "
      ideal   model   delta    sigma   weight residual
     113.18  105.10    8.08 2.37e+00 1.78e-01 1.16e+01
  angle pdb=" C   ASP A 460 "
        pdb=" N   LYS A 461 "
        pdb=" CA  LYS A 461 "
      ideal   model   delta    sigma   weight residual
     122.37  125.20   -2.83 9.30e-01 1.16e+00 9.24e+00
  angle pdb=" CA  ARG A 899 "
        pdb=" CB  ARG A 899 "
        pdb=" CG  ARG A 899 "
      ideal   model   delta    sigma   weight residual
     114.10  120.10   -6.00 2.00e+00 2.50e-01 9.01e+00
  angle pdb=" N   GLN A 162 "
        pdb=" CA  GLN A 162 "
        pdb=" C   GLN A 162 "
      ideal   model   delta    sigma   weight residual
     110.65  114.25   -3.60 1.26e+00 6.30e-01 8.15e+00
  angle pdb=" N   GLY A 721 "
        pdb=" CA  GLY A 721 "
        pdb=" C   GLY A 721 "
      ideal   model   delta    sigma   weight residual
     110.86  115.81   -4.95 1.84e+00 2.95e-01 7.24e+00
  ... (remaining 9134 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.11: 3568
       16.11 -    32.22: 316
       32.22 -    48.32: 69
       48.32 -    64.43: 10
       64.43 -    80.54: 6
  Dihedral angle restraints: 3969
    sinusoidal: 1570
      harmonic: 2399
  Sorted by residual:
  dihedral pdb=" CB  CYS A 446 "
           pdb=" SG  CYS A 446 "
           pdb=" SG  CYS A 455 "
           pdb=" CB  CYS A 455 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.03   54.97     1      1.00e+01 1.00e-02 4.09e+01
  dihedral pdb=" CA  ASN A 745 "
           pdb=" C   ASN A 745 "
           pdb=" N   GLY A 746 "
           pdb=" CA  GLY A 746 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.67  -27.33     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  THR A 776 "
           pdb=" C   THR A 776 "
           pdb=" N   ASP A 777 "
           pdb=" CA  ASP A 777 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.02   22.98     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 3966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 563
       0.030 -    0.060: 238
       0.060 -    0.089: 84
       0.089 -    0.119: 45
       0.119 -    0.149: 10
  Chirality restraints: 940
  Sorted by residual:
  chirality pdb=" CA  ILE A 190 "
            pdb=" N   ILE A 190 "
            pdb=" C   ILE A 190 "
            pdb=" CB  ILE A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  ILE A 140 "
            pdb=" N   ILE A 140 "
            pdb=" C   ILE A 140 "
            pdb=" CB  ILE A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CG  LEU A 726 "
            pdb=" CB  LEU A 726 "
            pdb=" CD1 LEU A 726 "
            pdb=" CD2 LEU A 726 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 937 not shown)

  Planarity restraints: 1205
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 717 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.55e+00
        pdb=" CD  GLU A 717 "   -0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 717 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 717 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 799 "   -0.028 5.00e-02 4.00e+02   4.24e-02 2.87e+00
        pdb=" N   PRO A 800 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 800 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 800 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 633 "    0.028 5.00e-02 4.00e+02   4.19e-02 2.81e+00
        pdb=" N   PRO A 634 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 634 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 634 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1202 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 4132
        3.02 -     3.49: 6972
        3.49 -     3.96: 10447
        3.96 -     4.43: 11477
        4.43 -     4.90: 18938
  Nonbonded interactions: 51966
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 113 "
            pdb=" OD1 ASP A 114 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" O   ASN A 540 "
            pdb=" OD1 ASN A 540 "
     model   vdw
     2.555 3.040
  nonbonded pdb=" N   ILE A 101 "
            pdb=" O   ILE A 101 "
     model   vdw
     2.580 2.496
  nonbonded pdb=" N   GLN A 799 "
            pdb=" O   GLN A 799 "
     model   vdw
     2.589 2.496
  nonbonded pdb=" O   SER A 137 "
            pdb=" OG  SER A 137 "
     model   vdw
     2.599 3.040
  ... (remaining 51961 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.040
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0588
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6763  Z= 0.223
  Angle     :  0.659   8.076   9145  Z= 0.359
  Chirality :  0.042   0.149    940
  Planarity :  0.004   0.042   1205
  Dihedral  : 12.961  80.540   2454
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.67 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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 are not related in a simple way.
  whole: -1.08 (0.30), residues: 838
  helix: -0.32 (0.84), residues: 39
  sheet: -0.44 (0.28), residues: 384
  loop : -0.94 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 775 
 TYR   0.022   0.002   TYR A 515 
 PHE   0.012   0.002   PHE A 441 
 TRP   0.014   0.001   TRP A 422 
 HIS   0.005   0.001   HIS A 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 6760)
  covalent geometry    : angle       0.65789 ( 9139)
  SS BOND              : bond        0.00643 (    3)
  SS BOND              : angle       1.75007 (    6)
  hydrogen bonds       : bond        0.20868 (  180)
  hydrogen bonds       : angle      10.62869 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 MET cc_start: -0.1243 (tpp) cc_final: -0.1581 (mmm)
REVERT: A  421 THR cc_start: 0.0908 (p) cc_final: 0.0344 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1235
  time to fit residues: 14.3459
Evaluate side-chains
  48 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 241 GLN
A 374 HIS
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
A 745 ASN
A 787 GLN
** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 807 ASN
** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 889 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.172509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.162263 restraints weight = 32904.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.164237 restraints weight = 21203.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.165621 restraints weight = 14987.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.166462 restraints weight = 11354.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.167120 restraints weight = 9253.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1057
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6763  Z= 0.143
  Angle     :  0.653   7.474   9145  Z= 0.343
  Chirality :  0.045   0.142    940
  Planarity :  0.004   0.044   1205
  Dihedral  :  4.835  26.153    951
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.76 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  7.21 %
    Favored  : 92.65 %
  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 are not related in a simple way.
  whole: -0.90 (0.29), residues: 838
  helix: -0.03 (0.85), residues: 40
  sheet: -0.19 (0.27), residues: 378
  loop : -0.98 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 341 
 TYR   0.016   0.002   TYR A 515 
 PHE   0.017   0.002   PHE A 398 
 TRP   0.017   0.002   TRP A 877 
 HIS   0.006   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6760)
  covalent geometry    : angle       0.65209 ( 9139)
  SS BOND              : bond        0.00191 (    3)
  SS BOND              : angle       1.36687 (    6)
  hydrogen bonds       : bond        0.03921 (  180)
  hydrogen bonds       : angle       7.07652 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 MET cc_start: -0.0308 (tpp) cc_final: -0.0922 (mmt)
REVERT: A  486 LYS cc_start: 0.5067 (tptt) cc_final: 0.4789 (tptt)
REVERT: A  764 MET cc_start: 0.0124 (pmm) cc_final: -0.3456 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1154
  time to fit residues: 9.1936
Evaluate side-chains
  45 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0570
   chunk 81 optimal weight:    7.9990
   overall best weight:    0.9900

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 333 HIS
A 442 GLN
A 481 GLN
** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.175098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.164946 restraints weight = 34213.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.166825 restraints weight = 22293.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.168106 restraints weight = 15814.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.169011 restraints weight = 12076.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.169470 restraints weight = 9816.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.4566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1168
moved from start:          0.5000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6763  Z= 0.118
  Angle     :  0.595   7.132   9145  Z= 0.312
  Chirality :  0.044   0.164    940
  Planarity :  0.004   0.071   1205
  Dihedral  :  4.537  23.499    951
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.80 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.44 %
    Favored  : 94.41 %
  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 are not related in a simple way.
  whole: -0.99 (0.29), residues: 838
  helix: -0.29 (0.84), residues: 40
  sheet: -0.24 (0.27), residues: 381
  loop : -1.03 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 432 
 TYR   0.015   0.001   TYR A 307 
 PHE   0.016   0.002   PHE A 696 
 TRP   0.010   0.001   TRP A 748 
 HIS   0.007   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6760)
  covalent geometry    : angle       0.59417 ( 9139)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       1.38236 (    6)
  hydrogen bonds       : bond        0.03723 (  180)
  hydrogen bonds       : angle       6.37681 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7455 (t0) cc_final: 0.6722 (t0)
REVERT: A  246 LEU cc_start: 0.7672 (tt) cc_final: 0.7390 (tp)
REVERT: A  343 MET cc_start: -0.0985 (tpp) cc_final: -0.1340 (mmt)
REVERT: A  764 MET cc_start: 0.0623 (pmm) cc_final: -0.3059 (ppp)
REVERT: A  804 TRP cc_start: 0.5849 (m-10) cc_final: 0.5612 (m100)
REVERT: A  809 MET cc_start: -0.3482 (mtt) cc_final: -0.3696 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1081
  time to fit residues: 8.2176
Evaluate side-chains
  47 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 70 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 76 optimal weight:    0.0030
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 287 GLN
A 481 GLN
A 621 HIS
** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.173974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.164737 restraints weight = 33495.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.166551 restraints weight = 21737.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.167828 restraints weight = 15338.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.168622 restraints weight = 11662.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.169354 restraints weight = 9476.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1145
moved from start:          0.5527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6763  Z= 0.098
  Angle     :  0.560  10.991   9145  Z= 0.290
  Chirality :  0.043   0.145    940
  Planarity :  0.004   0.041   1205
  Dihedral  :  4.332  23.183    951
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.88 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  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 are not related in a simple way.
  whole: -0.88 (0.29), residues: 838
  helix: -0.17 (0.80), residues: 40
  sheet: -0.13 (0.27), residues: 380
  loop : -1.00 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 407 
 TYR   0.012   0.001   TYR A 900 
 PHE   0.019   0.001   PHE A 300 
 TRP   0.008   0.001   TRP A 548 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6760)
  covalent geometry    : angle       0.55947 ( 9139)
  SS BOND              : bond        0.00550 (    3)
  SS BOND              : angle       0.93354 (    6)
  hydrogen bonds       : bond        0.03047 (  180)
  hydrogen bonds       : angle       5.99581 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 LYS cc_start: 0.4959 (tptt) cc_final: 0.4551 (tptt)
REVERT: A  764 MET cc_start: 0.0753 (pmm) cc_final: -0.2117 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1064
  time to fit residues: 7.8973
Evaluate side-chains
  42 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 80 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 287 GLN
A 481 GLN
** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.173784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.164535 restraints weight = 34336.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.166464 restraints weight = 22503.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.167798 restraints weight = 15807.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.168731 restraints weight = 11813.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.169416 restraints weight = 9428.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1278
moved from start:          0.6200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6763  Z= 0.104
  Angle     :  0.568   8.772   9145  Z= 0.296
  Chirality :  0.044   0.141    940
  Planarity :  0.004   0.050   1205
  Dihedral  :  4.344  23.285    951
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.04 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.09 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.29), residues: 838
  helix: -0.25 (0.79), residues: 40
  sheet: -0.03 (0.28), residues: 369
  loop : -1.07 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 102 
 TYR   0.012   0.001   TYR A 307 
 PHE   0.013   0.001   PHE A 300 
 TRP   0.009   0.001   TRP A 748 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 6760)
  covalent geometry    : angle       0.56791 ( 9139)
  SS BOND              : bond        0.00301 (    3)
  SS BOND              : angle       1.12756 (    6)
  hydrogen bonds       : bond        0.03077 (  180)
  hydrogen bonds       : angle       5.96831 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7362 (t0) cc_final: 0.6366 (t0)
REVERT: A  486 LYS cc_start: 0.4922 (tptt) cc_final: 0.4558 (tptt)
REVERT: A  764 MET cc_start: 0.1561 (pmm) cc_final: -0.1682 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0851
  time to fit residues: 6.5438
Evaluate side-chains
  46 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 GLN
A 477 HIS
A 481 GLN
A 737 ASN
** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 891 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.174954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.165222 restraints weight = 35808.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.167114 restraints weight = 23253.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.168354 restraints weight = 16451.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.169272 restraints weight = 12479.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.169934 restraints weight = 9973.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.4609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1897
moved from start:          0.8214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6763  Z= 0.174
  Angle     :  0.744   8.975   9145  Z= 0.389
  Chirality :  0.049   0.199    940
  Planarity :  0.005   0.053   1205
  Dihedral  :  5.679  27.532    951
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.47 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.29), residues: 838
  helix: -1.06 (0.74), residues: 42
  sheet: -0.18 (0.28), residues: 365
  loop : -1.55 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 706 
 TYR   0.023   0.002   TYR A 725 
 PHE   0.024   0.003   PHE A 398 
 TRP   0.025   0.002   TRP A 755 
 HIS   0.009   0.002   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6760)
  covalent geometry    : angle       0.74303 ( 9139)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       1.62147 (    6)
  hydrogen bonds       : bond        0.04263 (  180)
  hydrogen bonds       : angle       7.31779 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ARG cc_start: 0.4680 (mpp80) cc_final: 0.0788 (tpp-160)
REVERT: A  244 ASN cc_start: 0.7313 (t0) cc_final: 0.6401 (t0)
REVERT: A  580 LYS cc_start: 0.3958 (tttt) cc_final: 0.3340 (tptt)
REVERT: A  602 LEU cc_start: 0.6713 (tp) cc_final: 0.4975 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1228
  time to fit residues: 9.3767
Evaluate side-chains
  45 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 77 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0040
   chunk 42 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
A 512 HIS
** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 889 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.177191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.167686 restraints weight = 34907.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.169600 restraints weight = 22680.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.170816 restraints weight = 15886.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.171686 restraints weight = 11997.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.172106 restraints weight = 9486.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.4633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1746
moved from start:          0.8470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6763  Z= 0.101
  Angle     :  0.593   7.119   9145  Z= 0.307
  Chirality :  0.044   0.144    940
  Planarity :  0.004   0.047   1205
  Dihedral  :  4.781  22.701    951
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.68 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.29), residues: 838
  helix: -0.67 (0.78), residues: 40
  sheet: -0.17 (0.28), residues: 365
  loop : -1.53 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 603 
 TYR   0.018   0.001   TYR A 853 
 PHE   0.018   0.002   PHE A 398 
 TRP   0.011   0.001   TRP A 626 
 HIS   0.004   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 6760)
  covalent geometry    : angle       0.59271 ( 9139)
  SS BOND              : bond        0.00159 (    3)
  SS BOND              : angle       0.45006 (    6)
  hydrogen bonds       : bond        0.03204 (  180)
  hydrogen bonds       : angle       6.57947 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ARG cc_start: 0.4225 (mpp80) cc_final: 0.1011 (tpm170)
REVERT: A  244 ASN cc_start: 0.7324 (t0) cc_final: 0.6322 (t0)
REVERT: A  580 LYS cc_start: 0.3396 (tttt) cc_final: 0.2960 (tptt)
REVERT: A  626 TRP cc_start: 0.3344 (m-90) cc_final: 0.2900 (m-10)
REVERT: A  725 TYR cc_start: 0.0363 (m-10) cc_final: -0.0168 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1008
  time to fit residues: 7.7610
Evaluate side-chains
  45 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 73 optimal weight:    0.0980
   chunk 13 optimal weight:    6.9990
   chunk 9 optimal weight:    0.5980
   chunk 80 optimal weight:    0.2980
   chunk 74 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
** A 882 GLN ** 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 = 0.4786 r_free = 0.4786 target = 0.177651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.168091 restraints weight = 35425.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.170041 restraints weight = 23354.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.171372 restraints weight = 16524.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.172242 restraints weight = 12385.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.172967 restraints weight = 9875.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.4652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1713
moved from start:          0.8742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6763  Z= 0.099
  Angle     :  0.569   8.379   9145  Z= 0.295
  Chirality :  0.044   0.254    940
  Planarity :  0.004   0.049   1205
  Dihedral  :  4.584  22.235    951
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.80 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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 are not related in a simple way.
  whole: -1.38 (0.28), residues: 838
  helix: -0.86 (0.75), residues: 40
  sheet: -0.19 (0.28), residues: 369
  loop : -1.58 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 863 
 TYR   0.017   0.001   TYR A 853 
 PHE   0.018   0.001   PHE A 696 
 TRP   0.011   0.001   TRP A 626 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 6760)
  covalent geometry    : angle       0.56895 ( 9139)
  SS BOND              : bond        0.00200 (    3)
  SS BOND              : angle       0.49899 (    6)
  hydrogen bonds       : bond        0.03041 (  180)
  hydrogen bonds       : angle       6.39830 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.1729 (tmtt) cc_final: 0.1328 (tptt)
REVERT: A   77 ARG cc_start: 0.4504 (mpp80) cc_final: 0.1259 (tpm170)
REVERT: A  244 ASN cc_start: 0.7352 (t0) cc_final: 0.6317 (t0)
REVERT: A  580 LYS cc_start: 0.3393 (tttt) cc_final: 0.3023 (tptt)
REVERT: A  764 MET cc_start: 0.1086 (pmm) cc_final: 0.0883 (pmm)
REVERT: A  774 ASP cc_start: 0.7460 (p0) cc_final: 0.7239 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0952
  time to fit residues: 6.7207
Evaluate side-chains
  43 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 70 optimal weight:    0.3980
   chunk 83 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 382 ASN
** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4742 r_free = 0.4742 target = 0.173651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.164584 restraints weight = 36671.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.166427 restraints weight = 23807.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.167686 restraints weight = 16507.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.168644 restraints weight = 12157.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.169250 restraints weight = 9309.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2511
moved from start:          1.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6763  Z= 0.226
  Angle     :  0.934  10.245   9145  Z= 0.490
  Chirality :  0.056   0.295    940
  Planarity :  0.007   0.106   1205
  Dihedral  :  6.973  30.725    951
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 26.45
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 10.14 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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 are not related in a simple way.
  whole: -2.22 (0.27), residues: 838
  helix: -1.61 (0.71), residues: 42
  sheet: -0.69 (0.28), residues: 345
  loop : -2.14 (0.25), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 341 
 TYR   0.031   0.003   TYR A 326 
 PHE   0.020   0.003   PHE A 398 
 TRP   0.035   0.003   TRP A 748 
 HIS   0.011   0.003   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 6760)
  covalent geometry    : angle       0.93336 ( 9139)
  SS BOND              : bond        0.00562 (    3)
  SS BOND              : angle       1.60212 (    6)
  hydrogen bonds       : bond        0.05012 (  180)
  hydrogen bonds       : angle       8.99903 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.1038 (tmtt) cc_final: 0.0759 (tptt)
REVERT: A   77 ARG cc_start: 0.4266 (mpp80) cc_final: 0.0513 (tpp-160)
REVERT: A  244 ASN cc_start: 0.7397 (t0) cc_final: 0.6579 (t0)
REVERT: A  580 LYS cc_start: 0.4415 (tttt) cc_final: 0.4143 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1232
  time to fit residues: 10.0409
Evaluate side-chains
  52 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 31 optimal weight:    0.3980
   chunk 33 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 GLN
** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 882 GLN ** 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 = 0.4762 r_free = 0.4762 target = 0.175168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.166567 restraints weight = 35822.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.168393 restraints weight = 22787.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.169616 restraints weight = 15589.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.170446 restraints weight = 11418.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.171074 restraints weight = 8852.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.4645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2462
moved from start:          1.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6763  Z= 0.155
  Angle     :  0.737   8.762   9145  Z= 0.388
  Chirality :  0.049   0.194    940
  Planarity :  0.005   0.067   1205
  Dihedral  :  5.967  23.423    951
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.95 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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 are not related in a simple way.
  whole: -2.30 (0.27), residues: 838
  helix: -1.19 (0.74), residues: 42
  sheet: -0.98 (0.28), residues: 355
  loop : -2.04 (0.26), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 649 
 TYR   0.020   0.002   TYR A 473 
 PHE   0.016   0.002   PHE A 648 
 TRP   0.014   0.002   TRP A 845 
 HIS   0.012   0.002   HIS A 495 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6760)
  covalent geometry    : angle       0.73647 ( 9139)
  SS BOND              : bond        0.00339 (    3)
  SS BOND              : angle       0.90735 (    6)
  hydrogen bonds       : bond        0.03902 (  180)
  hydrogen bonds       : angle       8.15421 (  495)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.1465 (tmtt) cc_final: 0.1031 (tptt)
REVERT: A   77 ARG cc_start: 0.4032 (mpp80) cc_final: 0.0841 (tpm170)
REVERT: A  244 ASN cc_start: 0.7557 (t0) cc_final: 0.6589 (t0)
REVERT: A  580 LYS cc_start: 0.4392 (tttt) cc_final: 0.4107 (tptt)
REVERT: A  870 MET cc_start: 0.1662 (ptt) cc_final: 0.1458 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1017
  time to fit residues: 7.6763
Evaluate side-chains
  46 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    0.0970
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 72 optimal weight:    0.2980
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 882 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 = 0.4783 r_free = 0.4783 target = 0.177354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.168885 restraints weight = 35532.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.170726 restraints weight = 22903.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.171911 restraints weight = 15687.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.172781 restraints weight = 11492.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.173426 restraints weight = 8858.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.4681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2162
moved from start:          1.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6763  Z= 0.105
  Angle     :  0.616   8.807   9145  Z= 0.323
  Chirality :  0.046   0.161    940
  Planarity :  0.004   0.059   1205
  Dihedral  :  5.082  22.798    951
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.11 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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 are not related in a simple way.
  whole: -2.12 (0.28), residues: 838
  helix: -0.71 (0.77), residues: 43
  sheet: -0.91 (0.27), residues: 367
  loop : -1.92 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 643 
 TYR   0.019   0.001   TYR A 473 
 PHE   0.020   0.002   PHE A 398 
 TRP   0.010   0.001   TRP A 755 
 HIS   0.005   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 6760)
  covalent geometry    : angle       0.61584 ( 9139)
  SS BOND              : bond        0.00195 (    3)
  SS BOND              : angle       0.37916 (    6)
  hydrogen bonds       : bond        0.03227 (  180)
  hydrogen bonds       : angle       7.06157 (  495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1181.14 seconds
wall clock time: 21 minutes 8.23 seconds (1268.23 seconds total)