Starting phenix.real_space_refine
on Fri Aug 22 18:11:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f25_50138/08_2025/9f25_50138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f25_50138/08_2025/9f25_50138.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f25_50138/08_2025/9f25_50138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f25_50138/08_2025/9f25_50138.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f25_50138/08_2025/9f25_50138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f25_50138/08_2025/9f25_50138.map"
  }
  resolution = 3.7
  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=   0.000 sd=   0.034
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      19      5.16       5
     C    4331      2.51       5
     N    1079      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6717
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 830, 6717
          Classifications: {'peptide': 830}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 28, 'TRANS': 801}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 1.72, per 1000 atoms: 0.26
  Number of scatterers: 6717
  At special positions: 0
  Unit cell: (105.95, 70.85, 109.85, 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      19     16.00
     O    1288      8.00
     N    1079      7.00
     C    4331      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 454 " distance=2.00

  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: 0.59
  Conformation dependent library (CDL) restraints added in 388.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      46.7% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 80 through 101
      removed outlier: 3.716A  pdb=" N   THR A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
    Processing helix  chain 'A' and resid 130 through 132
      No H-bonds generated for 'chain 'A' and resid 130 through 132'
    Processing helix  chain 'A' and resid 216 through 233
      removed outlier: 3.631A  pdb=" N   THR A 220 " --> pdb=" O   ASP A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 267
    Processing helix  chain 'A' and resid 268 through 274
      removed outlier: 3.543A  pdb=" N   PHE A 273 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE A 274 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 300
    Processing helix  chain 'A' and resid 309 through 322
      removed outlier: 3.570A  pdb=" N   MET A 313 " --> pdb=" O   SER A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 347
    Processing helix  chain 'A' and resid 350 through 359
    Processing helix  chain 'A' and resid 409 through 413
      removed outlier: 3.555A  pdb=" N   PHE A 413 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 496 through 505
    Processing helix  chain 'A' and resid 549 through 556
    Processing helix  chain 'A' and resid 571 through 578
    Processing helix  chain 'A' and resid 587 through 596
      removed outlier: 3.535A  pdb=" N   VAL A 591 " --> pdb=" O   SER A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 619
      removed outlier: 4.085A  pdb=" N   GLU A 608 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 641
    Processing helix  chain 'A' and resid 648 through 660
    Processing helix  chain 'A' and resid 661 through 663
      No H-bonds generated for 'chain 'A' and resid 661 through 663'
    Processing helix  chain 'A' and resid 687 through 721
    Processing helix  chain 'A' and resid 721 through 753
    Processing helix  chain 'A' and resid 755 through 763
    Processing helix  chain 'A' and resid 765 through 800
      removed outlier: 3.661A  pdb=" N   LEU A 769 " --> pdb=" O   ASN A 765 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ASN A 783 " --> pdb=" O   LYS A 779 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A 796 " --> pdb=" O   SER A 792 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET A 800 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 824
      removed outlier: 3.557A  pdb=" N   GLY A 804 " --> pdb=" O   MET A 800 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASP A 817 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA A 818 " --> pdb=" O   SER A 814 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR A 824 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 846
    Processing helix  chain 'A' and resid 852 through 856
      removed outlier: 3.606A  pdb=" N   LYS A 855 " --> pdb=" O   GLN A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 868
      removed outlier: 4.217A  pdb=" N   GLU A 868 " --> pdb=" O   SER A 864 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148
      removed outlier: 4.225A  pdb=" N   TYR A  21 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   LYS A  34 " --> pdb=" O   PRO A  46 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ILE A  42 " --> pdb=" O   ILE A  38 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY A 155 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   GLU A  47 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL A 152 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 214
    Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 325
    Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 458
      removed outlier: 9.270A  pdb=" N   TYR A 543 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU A 428 " --> pdb=" O   TYR A 543 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 481
    Processing sheet with id=AA7, first strand: chain 'A' and resid 567 through 569
      removed outlier: 6.411A  pdb=" N   ALA A 567 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    301 hydrogen bonds defined for protein.
    873 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: 1.07

  Time building geometry restraints manager: 0.79 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: 2141
        1.35 -     1.47: 1669
        1.47 -     1.59: 3019
        1.59 -     1.71: 0
        1.71 -     1.83: 33
  Bond restraints: 6862
  Sorted by residual:
  bond pdb=" C   ALA A 601 "
       pdb=" N   MET A 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.376 -0.044 1.29e-02 6.01e+03 1.16e+01
  bond pdb=" C   VAL A 611 "
       pdb=" N   TYR A 612 "
    ideal  model  delta    sigma   weight residual
    1.335  1.371 -0.036 1.36e-02 5.41e+03 7.15e+00
  bond pdb=" C   LYS A 456 "
       pdb=" N   VAL A 457 "
    ideal  model  delta    sigma   weight residual
    1.331  1.309  0.021 1.27e-02 6.20e+03 2.86e+00
  bond pdb=" CB  GLU A 708 "
       pdb=" CG  GLU A 708 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CB  GLU A 535 "
       pdb=" CG  GLU A 535 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.64e-01
  ... (remaining 6857 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 9183
        2.00 -     4.00: 91
        4.00 -     5.99: 18
        5.99 -     7.99: 1
        7.99 -     9.99: 1
  Bond angle restraints: 9294
  Sorted by residual:
  angle pdb=" CB  MET A 646 "
        pdb=" CG  MET A 646 "
        pdb=" SD  MET A 646 "
      ideal   model   delta    sigma   weight residual
     112.70  102.71    9.99 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" CA  GLU A 708 "
        pdb=" CB  GLU A 708 "
        pdb=" CG  GLU A 708 "
      ideal   model   delta    sigma   weight residual
     114.10  119.23   -5.13 2.00e+00 2.50e-01 6.58e+00
  angle pdb=" CB  GLU A 708 "
        pdb=" CG  GLU A 708 "
        pdb=" CD  GLU A 708 "
      ideal   model   delta    sigma   weight residual
     112.60  116.93   -4.33 1.70e+00 3.46e-01 6.50e+00
  angle pdb=" CA  MET A 646 "
        pdb=" CB  MET A 646 "
        pdb=" CG  MET A 646 "
      ideal   model   delta    sigma   weight residual
     114.10  119.06   -4.96 2.00e+00 2.50e-01 6.16e+00
  angle pdb=" CA  GLN A 753 "
        pdb=" CB  GLN A 753 "
        pdb=" CG  GLN A 753 "
      ideal   model   delta    sigma   weight residual
     114.10  118.95   -4.85 2.00e+00 2.50e-01 5.89e+00
  ... (remaining 9289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 3531
       17.77 -    35.53: 444
       35.53 -    53.29: 107
       53.29 -    71.06: 20
       71.06 -    88.82: 9
  Dihedral angle restraints: 4111
    sinusoidal: 1656
      harmonic: 2455
  Sorted by residual:
  dihedral pdb=" CB  CYS A 430 "
           pdb=" SG  CYS A 430 "
           pdb=" SG  CYS A 454 "
           pdb=" CB  CYS A 454 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.47   34.53     1      1.00e+01 1.00e-02 1.69e+01
  dihedral pdb=" CA  MET A 646 "
           pdb=" C   MET A 646 "
           pdb=" N   LEU A 647 "
           pdb=" CA  LEU A 647 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.01  -18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  ALA A  20 "
           pdb=" C   ALA A  20 "
           pdb=" N   TYR A  21 "
           pdb=" CA  TYR A  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.39   17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 4108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 680
       0.031 -    0.062: 230
       0.062 -    0.093: 77
       0.093 -    0.124: 41
       0.124 -    0.155: 8
  Chirality restraints: 1036
  Sorted by residual:
  chirality pdb=" CB  ILE A 633 "
            pdb=" CA  ILE A 633 "
            pdb=" CG1 ILE A 633 "
            pdb=" CG2 ILE A 633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CA  ILE A 154 "
            pdb=" N   ILE A 154 "
            pdb=" C   ILE A 154 "
            pdb=" CB  ILE A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  ILE A  19 "
            pdb=" N   ILE A  19 "
            pdb=" C   ILE A  19 "
            pdb=" CB  ILE A  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 1033 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 634 "   -0.038 5.00e-02 4.00e+02   5.93e-02 5.63e+00
        pdb=" N   PRO A 635 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 635 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 635 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 753 "    0.009 2.00e-02 2.50e+03   1.79e-02 3.19e+00
        pdb=" C   GLN A 753 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLN A 753 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 754 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  24 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A  25 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A  25 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  25 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 540
        2.74 -     3.28: 6962
        3.28 -     3.82: 11164
        3.82 -     4.36: 12487
        4.36 -     4.90: 22017
  Nonbonded interactions: 53170
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 121 "
            pdb=" OE2 GLU A 126 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OH  TYR A 583 "
            pdb=" O   PRO A 639 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   GLY A 179 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NE2 HIS A 230 "
            pdb=" O   LEU A 345 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD1 ASP A 726 "
            pdb=" NH2 ARG A 729 "
     model   vdw
     2.278 3.120
  ... (remaining 53165 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:             2.830
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.880
  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:             0.010
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
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      :  0.002   0.044   6863  Z= 0.120
  Angle     :  0.533   9.988   9296  Z= 0.279
  Chirality :  0.040   0.155   1036
  Planarity :  0.004   0.059   1194
  Dihedral  : 16.769  88.824   2524
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 22.89 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.30), residues: 822
  helix:  1.97 (0.28), residues: 370
  sheet: -0.58 (0.55), residues: 79
  loop : -1.07 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 702 
 TYR   0.013   0.001   TYR A 636 
 PHE   0.013   0.001   PHE A 366 
 TRP   0.013   0.001   TRP A 606 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6862)
  covalent geometry    : angle       0.52756 ( 9294)
  SS BOND              : bond        0.03197 (    1)
  SS BOND              : angle       5.13780 (    2)
  hydrogen bonds       : bond        0.13764 (  301)
  hydrogen bonds       : angle       5.03809 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0753
  time to fit residues: 9.7684
Evaluate side-chains
  81 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
A 133 ASN
A 470 ASN
A 533 ASN
A 539 ASN
A 642 ASN
A 693 GLN
A 748 ASN
A 763 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.156746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131738 restraints weight = 10943.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.135820 restraints weight = 6481.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.138651 restraints weight = 4568.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.140411 restraints weight = 3575.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.141762 restraints weight = 3025.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6863  Z= 0.163
  Angle     :  0.539   7.793   9296  Z= 0.283
  Chirality :  0.042   0.166   1036
  Planarity :  0.004   0.037   1194
  Dihedral  :  3.873  18.538    891
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.88 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.29), residues: 822
  helix:  2.13 (0.28), residues: 365
  sheet: -0.60 (0.58), residues: 67
  loop : -0.92 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  48 
 TYR   0.013   0.001   TYR A 384 
 PHE   0.010   0.001   PHE A 652 
 TRP   0.009   0.001   TRP A 606 
 HIS   0.005   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6862)
  covalent geometry    : angle       0.53831 ( 9294)
  SS BOND              : bond        0.01122 (    1)
  SS BOND              : angle       1.68409 (    2)
  hydrogen bonds       : bond        0.04286 (  301)
  hydrogen bonds       : angle       4.24953 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 TYR cc_start: 0.8457 (t80) cc_final: 0.8176 (t80)
REVERT: A  681 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7880 (mt)
REVERT: A  732 MET cc_start: 0.8082 (tpt) cc_final: 0.7822 (tpt)
REVERT: A  801 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6500 (mm)
  outliers start: 23
  outliers final: 15
  residues processed: 105
  average time/residue: 0.0714
  time to fit residues: 10.6273
Evaluate side-chains
  100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  863 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    0.2980
   chunk 62 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A 133 ASN
A 693 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.155152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.130419 restraints weight = 10596.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.134393 restraints weight = 6500.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137101 restraints weight = 4634.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.138994 restraints weight = 3656.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.140235 restraints weight = 3079.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6863  Z= 0.118
  Angle     :  0.511  10.806   9296  Z= 0.264
  Chirality :  0.041   0.167   1036
  Planarity :  0.003   0.035   1194
  Dihedral  :  3.818  20.652    891
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.02 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.30), residues: 822
  helix:  2.25 (0.28), residues: 365
  sheet: -0.53 (0.59), residues: 67
  loop : -0.92 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  48 
 TYR   0.011   0.001   TYR A 636 
 PHE   0.008   0.001   PHE A  36 
 TRP   0.010   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6862)
  covalent geometry    : angle       0.51097 ( 9294)
  SS BOND              : bond        0.00700 (    1)
  SS BOND              : angle       1.46668 (    2)
  hydrogen bonds       : bond        0.03776 (  301)
  hydrogen bonds       : angle       4.02735 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 TYR cc_start: 0.8484 (t80) cc_final: 0.8234 (t80)
REVERT: A  697 ASN cc_start: 0.6663 (m-40) cc_final: 0.6323 (t0)
REVERT: A  801 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6383 (mm)
  outliers start: 22
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0645
  time to fit residues: 10.5296
Evaluate side-chains
  101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  845 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
A 224 GLN
A 400 ASN
A 642 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.155730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.130859 restraints weight = 10764.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.134898 restraints weight = 6542.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.137665 restraints weight = 4652.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.139395 restraints weight = 3659.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.140817 restraints weight = 3109.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6863  Z= 0.116
  Angle     :  0.501   8.513   9296  Z= 0.257
  Chirality :  0.041   0.172   1036
  Planarity :  0.003   0.036   1194
  Dihedral  :  3.766  21.809    891
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 21.15 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.30), residues: 822
  helix:  2.28 (0.28), residues: 366
  sheet: -0.52 (0.59), residues: 67
  loop : -0.94 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  48 
 TYR   0.011   0.001   TYR A 321 
 PHE   0.007   0.001   PHE A 290 
 TRP   0.013   0.001   TRP A 606 
 HIS   0.005   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6862)
  covalent geometry    : angle       0.50012 ( 9294)
  SS BOND              : bond        0.00458 (    1)
  SS BOND              : angle       1.49749 (    2)
  hydrogen bonds       : bond        0.03616 (  301)
  hydrogen bonds       : angle       3.90463 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 LYS cc_start: 0.8004 (pptt) cc_final: 0.7623 (mmtt)
REVERT: A  312 TYR cc_start: 0.8507 (t80) cc_final: 0.8248 (t80)
REVERT: A  456 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7521 (mtpp)
REVERT: A  697 ASN cc_start: 0.6600 (m-40) cc_final: 0.6319 (t0)
REVERT: A  801 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6372 (mm)
  outliers start: 28
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0649
  time to fit residues: 10.4281
Evaluate side-chains
  103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  863 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 60 optimal weight:    0.3980
   chunk 26 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0270
   overall best weight:    1.6844

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.149419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.124612 restraints weight = 10895.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128482 restraints weight = 6702.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131118 restraints weight = 4820.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.132919 restraints weight = 3839.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.133982 restraints weight = 3266.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6863  Z= 0.185
  Angle     :  0.562   7.887   9296  Z= 0.289
  Chirality :  0.043   0.219   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  4.023  22.654    891
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 20.35 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.29), residues: 822
  helix:  1.94 (0.27), residues: 365
  sheet: -0.55 (0.54), residues: 79
  loop : -1.17 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  48 
 TYR   0.015   0.002   TYR A 384 
 PHE   0.011   0.002   PHE A 585 
 TRP   0.011   0.001   TRP A 606 
 HIS   0.005   0.002   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6862)
  covalent geometry    : angle       0.56106 ( 9294)
  SS BOND              : bond        0.00989 (    1)
  SS BOND              : angle       1.88569 (    2)
  hydrogen bonds       : bond        0.04043 (  301)
  hydrogen bonds       : angle       4.06055 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  312 TYR cc_start: 0.8583 (t80) cc_final: 0.8349 (t80)
REVERT: A  456 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7620 (mtpp)
REVERT: A  681 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7809 (mt)
REVERT: A  697 ASN cc_start: 0.6676 (m-40) cc_final: 0.6376 (t0)
REVERT: A  774 ASN cc_start: 0.7226 (m-40) cc_final: 0.6997 (t0)
REVERT: A  801 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6523 (mm)
  outliers start: 38
  outliers final: 25
  residues processed: 116
  average time/residue: 0.0733
  time to fit residues: 11.9542
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  602 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 74 optimal weight:    0.6980
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.153103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.128763 restraints weight = 10836.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.132710 restraints weight = 6599.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.135334 restraints weight = 4726.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.137120 restraints weight = 3751.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.138314 restraints weight = 3179.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6863  Z= 0.143
  Angle     :  0.529   6.972   9296  Z= 0.274
  Chirality :  0.042   0.214   1036
  Planarity :  0.003   0.041   1194
  Dihedral  :  3.945  21.853    891
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 21.02 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.29), residues: 822
  helix:  2.11 (0.28), residues: 360
  sheet: -0.67 (0.57), residues: 72
  loop : -1.12 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 729 
 TYR   0.012   0.001   TYR A 384 
 PHE   0.009   0.001   PHE A 338 
 TRP   0.011   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6862)
  covalent geometry    : angle       0.52812 ( 9294)
  SS BOND              : bond        0.01008 (    1)
  SS BOND              : angle       1.90526 (    2)
  hydrogen bonds       : bond        0.03759 (  301)
  hydrogen bonds       : angle       4.00422 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 89
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 LYS cc_start: 0.8045 (pptt) cc_final: 0.7787 (mmtt)
REVERT: A  312 TYR cc_start: 0.8556 (t80) cc_final: 0.8322 (t80)
REVERT: A  456 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7611 (mtpp)
REVERT: A  697 ASN cc_start: 0.6640 (m-40) cc_final: 0.6359 (t0)
REVERT: A  801 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6372 (mm)
  outliers start: 34
  outliers final: 24
  residues processed: 116
  average time/residue: 0.0661
  time to fit residues: 11.1271
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0770
   chunk 73 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0270
   chunk 44 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.8202

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 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 = 0.3947 r_free = 0.3947 target = 0.154238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130257 restraints weight = 10550.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134093 restraints weight = 6512.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.136702 restraints weight = 4698.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.138461 restraints weight = 3724.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.139415 restraints weight = 3163.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6863  Z= 0.119
  Angle     :  0.550  13.027   9296  Z= 0.274
  Chirality :  0.041   0.184   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  3.857  21.589    891
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.82 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.30), residues: 822
  helix:  2.24 (0.28), residues: 360
  sheet: -0.57 (0.58), residues: 72
  loop : -1.06 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 729 
 TYR   0.011   0.001   TYR A 384 
 PHE   0.009   0.001   PHE A 338 
 TRP   0.013   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6862)
  covalent geometry    : angle       0.54998 ( 9294)
  SS BOND              : bond        0.00677 (    1)
  SS BOND              : angle       1.68458 (    2)
  hydrogen bonds       : bond        0.03577 (  301)
  hydrogen bonds       : angle       3.91586 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  312 TYR cc_start: 0.8534 (t80) cc_final: 0.8289 (t80)
REVERT: A  456 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7627 (mtpp)
REVERT: A  697 ASN cc_start: 0.6602 (m-40) cc_final: 0.6348 (t0)
REVERT: A  801 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6389 (mm)
  outliers start: 27
  outliers final: 22
  residues processed: 111
  average time/residue: 0.0681
  time to fit residues: 10.9979
Evaluate side-chains
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  602 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0980
   chunk 33 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0040
   chunk 39 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 78 optimal weight:    4.9990
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.157948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.133624 restraints weight = 10683.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.137556 restraints weight = 6614.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140218 restraints weight = 4742.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.142007 restraints weight = 3752.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.143235 restraints weight = 3173.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6863  Z= 0.103
  Angle     :  0.535  12.252   9296  Z= 0.267
  Chirality :  0.041   0.171   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  3.773  21.057    891
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.16 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.30), residues: 822
  helix:  2.34 (0.28), residues: 359
  sheet: -0.52 (0.58), residues: 72
  loop : -1.00 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 729 
 TYR   0.015   0.001   TYR A 856 
 PHE   0.008   0.001   PHE A 194 
 TRP   0.015   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6862)
  covalent geometry    : angle       0.53511 ( 9294)
  SS BOND              : bond        0.00992 (    1)
  SS BOND              : angle       1.44962 (    2)
  hydrogen bonds       : bond        0.03418 (  301)
  hydrogen bonds       : angle       3.85842 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 TYR cc_start: 0.8506 (t80) cc_final: 0.8226 (t80)
REVERT: A  456 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7623 (mtpp)
REVERT: A  697 ASN cc_start: 0.6593 (m-40) cc_final: 0.6327 (t0)
REVERT: A  801 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6341 (mm)
  outliers start: 20
  outliers final: 17
  residues processed: 111
  average time/residue: 0.0670
  time to fit residues: 10.9106
Evaluate side-chains
  105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.151530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127141 restraints weight = 10760.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.130904 restraints weight = 6662.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.133294 restraints weight = 4823.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.135061 restraints weight = 3892.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136210 restraints weight = 3319.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6863  Z= 0.186
  Angle     :  0.613  11.046   9296  Z= 0.308
  Chirality :  0.043   0.176   1036
  Planarity :  0.003   0.042   1194
  Dihedral  :  4.049  21.528    891
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.09 %
    Favored  : 73.76 %
  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 aren not related in a simple way.
  whole:  0.49 (0.29), residues: 822
  helix:  2.01 (0.28), residues: 360
  sheet: -0.67 (0.59), residues: 72
  loop : -1.15 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  97 
 TYR   0.015   0.002   TYR A 856 
 PHE   0.018   0.002   PHE A 366 
 TRP   0.014   0.001   TRP A 706 
 HIS   0.005   0.002   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6862)
  covalent geometry    : angle       0.61248 ( 9294)
  SS BOND              : bond        0.00794 (    1)
  SS BOND              : angle       1.92008 (    2)
  hydrogen bonds       : bond        0.03952 (  301)
  hydrogen bonds       : angle       4.05500 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 LYS cc_start: 0.8020 (pptt) cc_final: 0.7747 (mmtt)
REVERT: A  312 TYR cc_start: 0.8601 (t80) cc_final: 0.8365 (t80)
REVERT: A  456 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7671 (mtpp)
REVERT: A  697 ASN cc_start: 0.6692 (m-40) cc_final: 0.6416 (t0)
REVERT: A  801 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6484 (mm)
  outliers start: 31
  outliers final: 27
  residues processed: 109
  average time/residue: 0.0716
  time to fit residues: 11.1172
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  602 MET
Chi-restraints excluded: chain A residue  646 MET
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
A 642 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.155428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130856 restraints weight = 10619.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.134762 restraints weight = 6498.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137415 restraints weight = 4641.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.139125 restraints weight = 3671.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140536 restraints weight = 3117.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6863  Z= 0.125
  Angle     :  0.577  11.195   9296  Z= 0.286
  Chirality :  0.042   0.232   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  3.952  21.231    891
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.16 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.30), residues: 822
  helix:  2.16 (0.28), residues: 360
  sheet: -0.61 (0.59), residues: 72
  loop : -1.07 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 702 
 TYR   0.013   0.001   TYR A 856 
 PHE   0.015   0.001   PHE A 366 
 TRP   0.010   0.001   TRP A 606 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6862)
  covalent geometry    : angle       0.57649 ( 9294)
  SS BOND              : bond        0.00826 (    1)
  SS BOND              : angle       1.91759 (    2)
  hydrogen bonds       : bond        0.03590 (  301)
  hydrogen bonds       : angle       4.01532 (  873)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 LYS cc_start: 0.8013 (pptt) cc_final: 0.7744 (mmtt)
REVERT: A  312 TYR cc_start: 0.8568 (t80) cc_final: 0.8289 (t80)
REVERT: A  456 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7651 (mtpp)
REVERT: A  697 ASN cc_start: 0.6663 (m-40) cc_final: 0.6418 (t0)
REVERT: A  801 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6386 (mm)
  outliers start: 24
  outliers final: 20
  residues processed: 102
  average time/residue: 0.0690
  time to fit residues: 10.0884
Evaluate side-chains
  102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  696 ASP
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  791 CYS
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  819 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 298 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 = 0.3969 r_free = 0.3969 target = 0.157301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131616 restraints weight = 10784.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.135746 restraints weight = 6561.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.138578 restraints weight = 4667.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.140494 restraints weight = 3676.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.141516 restraints weight = 3097.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6863  Z= 0.122
  Angle     :  0.577  11.889   9296  Z= 0.287
  Chirality :  0.042   0.221   1036
  Planarity :  0.003   0.040   1194
  Dihedral  :  3.899  21.753    891
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 23.29 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.29), residues: 822
  helix:  2.20 (0.28), residues: 360
  sheet: -0.55 (0.58), residues: 72
  loop : -1.08 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 702 
 TYR   0.012   0.001   TYR A 856 
 PHE   0.014   0.001   PHE A 366 
 TRP   0.018   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6862)
  covalent geometry    : angle       0.57663 ( 9294)
  SS BOND              : bond        0.00721 (    1)
  SS BOND              : angle       1.74727 (    2)
  hydrogen bonds       : bond        0.03525 (  301)
  hydrogen bonds       : angle       3.96413 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1386.14 seconds
wall clock time: 24 minutes 41.50 seconds (1481.50 seconds total)