Starting phenix.real_space_refine
on Wed Sep 17 06:15:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q76_18205/09_2025/8q76_18205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q76_18205/09_2025/8q76_18205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q76_18205/09_2025/8q76_18205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q76_18205/09_2025/8q76_18205.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q76_18205/09_2025/8q76_18205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q76_18205/09_2025/8q76_18205.map"
  }
  resolution = 3.29
  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=  -0.002 sd=   0.047
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: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      34      5.16       5
     Be      1      3.05       5
     C    3760      2.51       5
     N     975      2.21       5
     O    1095      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5869
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 774, 5868
          Classifications: {'peptide': 774}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 738}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.49, per 1000 atoms: 0.25
  Number of scatterers: 5869
  At special positions: 0
  Unit cell: (81.536, 83.2, 136.448, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      34     16.00
     Mg      1     11.99
     F       3      9.00
     O    1095      8.00
     N     975      7.00
     C    3760      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.56
  Conformation dependent library (CDL) restraints added in 348.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      51.9% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 197 through 210
      removed outlier: 3.738A  pdb=" N   ILE A 201 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 246
      removed outlier: 4.356A  pdb=" N   LEU A 240 " --> pdb=" O   GLY A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 296
      removed outlier: 4.252A  pdb=" N   ALA A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.795A  pdb=" N   TYR A 309 " --> pdb=" O   TRP A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 332
      Proline residue:  A 328  - end of helix
    Processing helix  chain 'A' and resid 334 through 344
    Processing helix  chain 'A' and resid 354 through 377
      removed outlier: 5.943A  pdb=" N   THR A 360 " --> pdb=" O   VAL A 356 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ASN A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 362 " --> pdb=" O   LEU A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 407
      removed outlier: 4.146A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 3.703A  pdb=" N   THR A 418 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA A 421 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 447
      No H-bonds generated for 'chain 'A' and resid 445 through 447'
    Processing helix  chain 'A' and resid 512 through 515
    Processing helix  chain 'A' and resid 516 through 530
    Processing helix  chain 'A' and resid 537 through 545
    Processing helix  chain 'A' and resid 546 through 567
    Processing helix  chain 'A' and resid 571 through 575
    Processing helix  chain 'A' and resid 580 through 596
      removed outlier: 3.672A  pdb=" N   VAL A 592 " --> pdb=" O   PHE A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 620
      removed outlier: 5.654A  pdb=" N   VAL A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 632
      removed outlier: 3.858A  pdb=" N   LEU A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 676
    Processing helix  chain 'A' and resid 680 through 697
    Processing helix  chain 'A' and resid 731 through 738
      removed outlier: 3.637A  pdb=" N   PHE A 738 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 748
    Processing helix  chain 'A' and resid 782 through 793
    Processing helix  chain 'A' and resid 804 through 816
    Processing helix  chain 'A' and resid 825 through 839
    Processing helix  chain 'A' and resid 849 through 851
      No H-bonds generated for 'chain 'A' and resid 849 through 851'
    Processing helix  chain 'A' and resid 852 through 859
    Processing helix  chain 'A' and resid 869 through 876
    Processing helix  chain 'A' and resid 885 through 900
      removed outlier: 3.870A  pdb=" N   ILE A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 922
      removed outlier: 4.266A  pdb=" N   TYR A 912 " --> pdb=" O   TRP A 908 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   ASN A 913 " --> pdb=" O   ALA A 909 " (cutoff:3.500A)
      Proline residue:  A 918  - end of helix
    Processing helix  chain 'A' and resid 934 through 939
      removed outlier: 4.002A  pdb=" N   GLY A 938 " --> pdb=" O   PRO A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 940 through 948
    Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 220
      removed outlier: 3.625A  pdb=" N   ASP A 220 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   THR A 225 " --> pdb=" O   ASP A 220 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASN A 255 " --> pdb=" O   GLU A 193 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 426
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453
      removed outlier: 7.460A  pdb=" N   ILE A 506 " --> pdb=" O   ILE A 468 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474
    Processing sheet with id=AA5, first strand: chain 'A' and resid 621 through 623
      removed outlier: 6.165A  pdb=" N   GLY A 862 " --> pdb=" O   ILE A 878 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   LEU A 880 " --> pdb=" O   GLY A 862 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ALA A 864 " --> pdb=" O   LEU A 880 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL A 861 " --> pdb=" O   VAL A 843 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET A 845 " --> pdb=" O   VAL A 861 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ALA A 637 " --> pdb=" O   ALA A 844 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   VAL A 846 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ILE A 639 " --> pdb=" O   VAL A 846 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ILE A 638 " --> pdb=" O   ILE A 798 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   VAL A 800 " --> pdb=" O   ILE A 638 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   PHE A 640 " --> pdb=" O   VAL A 800 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   SER A 797 " --> pdb=" O   THR A 819 " (cutoff:3.500A)
      removed outlier: 8.886A  pdb=" N   PHE A 821 " --> pdb=" O   SER A 797 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   MET A 799 " --> pdb=" O   PHE A 821 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 652 through 654
    Processing sheet with id=AA7, first strand: chain 'A' and resid 707 through 708

    291 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1098
        1.33 -     1.45: 1356
        1.45 -     1.57: 3471
        1.57 -     1.69: 1
        1.69 -     1.81: 54
  Bond restraints: 5980
  Sorted by residual:
  bond pdb=" OD1 BFD A 641 "
       pdb="BE   BFD A 641 "
    ideal  model  delta    sigma   weight residual
    1.737  1.533  0.204 2.00e-02 2.50e+03 1.04e+02
  bond pdb=" CA  ALA A 637 "
       pdb=" C   ALA A 637 "
    ideal  model  delta    sigma   weight residual
    1.522  1.458  0.063 1.21e-02 6.83e+03 2.74e+01
  bond pdb=" N   ILE A 638 "
       pdb=" CA  ILE A 638 "
    ideal  model  delta    sigma   weight residual
    1.457  1.400  0.057 1.14e-02 7.69e+03 2.50e+01
  bond pdb=" N   ALA A 637 "
       pdb=" CA  ALA A 637 "
    ideal  model  delta    sigma   weight residual
    1.454  1.411  0.044 1.27e-02 6.20e+03 1.19e+01
  bond pdb=" CA  ILE A 638 "
       pdb=" C   ILE A 638 "
    ideal  model  delta    sigma   weight residual
    1.522  1.483  0.039 1.20e-02 6.94e+03 1.07e+01
  ... (remaining 5975 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.93: 8075
        3.93 -     7.87: 42
        7.87 -    11.80: 5
       11.80 -    15.73: 0
       15.73 -    19.67: 2
  Bond angle restraints: 8124
  Sorted by residual:
  angle pdb=" O   BFD A 641 "
        pdb=" C   BFD A 641 "
        pdb=" N   LYS A 642 "
      ideal   model   delta    sigma   weight residual
     123.00  103.33   19.67 1.60e+00 3.91e-01 1.51e+02
  angle pdb=" CA  BFD A 641 "
        pdb=" C   BFD A 641 "
        pdb=" N   LYS A 642 "
      ideal   model   delta    sigma   weight residual
     116.20  134.22  -18.02 2.00e+00 2.50e-01 8.12e+01
  angle pdb=" C   PHE A 640 "
        pdb=" N   BFD A 641 "
        pdb=" CA  BFD A 641 "
      ideal   model   delta    sigma   weight residual
     121.70  111.61   10.09 1.80e+00 3.09e-01 3.15e+01
  angle pdb=" N   GLY A 748 "
        pdb=" CA  GLY A 748 "
        pdb=" C   GLY A 748 "
      ideal   model   delta    sigma   weight residual
     113.18  123.41  -10.23 2.37e+00 1.78e-01 1.86e+01
  angle pdb=" C   LYS A 636 "
        pdb=" N   ALA A 637 "
        pdb=" CA  ALA A 637 "
      ideal   model   delta    sigma   weight residual
     122.62  117.18    5.44 1.56e+00 4.11e-01 1.21e+01
  ... (remaining 8119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 3209
       15.92 -    31.85: 294
       31.85 -    47.77: 72
       47.77 -    63.70: 14
       63.70 -    79.62: 12
  Dihedral angle restraints: 3601
    sinusoidal: 1380
      harmonic: 2221
  Sorted by residual:
  dihedral pdb=" CA  SER A 301 "
           pdb=" C   SER A 301 "
           pdb=" N   PRO A 302 "
           pdb=" CA  PRO A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.83  -33.17     0      5.00e+00 4.00e-02 4.40e+01
  dihedral pdb=" CA  GLU A 752 "
           pdb=" C   GLU A 752 "
           pdb=" N   THR A 753 "
           pdb=" CA  THR A 753 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.90   33.10     0      5.00e+00 4.00e-02 4.38e+01
  dihedral pdb=" CA  LEU A 910 "
           pdb=" C   LEU A 910 "
           pdb=" N   GLY A 911 "
           pdb=" CA  GLY A 911 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.21   29.79     0      5.00e+00 4.00e-02 3.55e+01
  ... (remaining 3598 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 778
       0.059 -    0.118: 171
       0.118 -    0.177: 12
       0.177 -    0.236: 1
       0.236 -    0.295: 1
  Chirality restraints: 963
  Sorted by residual:
  chirality pdb=" CA  BFD A 641 "
            pdb=" N   BFD A 641 "
            pdb=" C   BFD A 641 "
            pdb=" CB  BFD A 641 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  VAL A 311 "
            pdb=" N   VAL A 311 "
            pdb=" C   VAL A 311 "
            pdb=" CB  VAL A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.90e-01
  chirality pdb=" CA  PRO A 302 "
            pdb=" N   PRO A 302 "
            pdb=" C   PRO A 302 "
            pdb=" CB  PRO A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.80e-01
  ... (remaining 960 not shown)

  Planarity restraints: 1027
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 640 "    0.019 2.00e-02 2.50e+03   4.03e-02 1.62e+01
        pdb=" C   PHE A 640 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PHE A 640 "    0.027 2.00e-02 2.50e+03
        pdb=" N   BFD A 641 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 236 "   -0.041 5.00e-02 4.00e+02   6.27e-02 6.30e+00
        pdb=" N   PRO A 237 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 237 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 237 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 297 "   -0.041 5.00e-02 4.00e+02   6.25e-02 6.26e+00
        pdb=" N   PRO A 298 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1024 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 63
        2.54 -     3.13: 5041
        3.13 -     3.72: 9719
        3.72 -     4.31: 12835
        4.31 -     4.90: 20738
  Nonbonded interactions: 48396
  Sorted by model distance:
  nonbonded pdb=" OD2 BFD A 641 "
            pdb="MG    MG A1001 "
     model   vdw
     1.945 2.170
  nonbonded pdb=" OD2 ASP A 848 "
            pdb="MG    MG A1001 "
     model   vdw
     2.048 2.170
  nonbonded pdb=" NH1 ARG A 269 "
            pdb=" O   GLY A 408 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS A 488 "
            pdb=" O   LYS A 493 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   ALA A 267 "
            pdb=" ND1 HIS A 271 "
     model   vdw
     2.275 3.120
  ... (remaining 48391 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 individual isotropic
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:             2.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.260
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.204   5980  Z= 0.249
  Angle     :  0.849  19.668   8124  Z= 0.452
  Chirality :  0.048   0.295    963
  Planarity :  0.007   0.063   1027
  Dihedral  : 14.275  79.622   2171
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 12.22 %
    Favored  : 87.26 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.16 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.14 %

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: -1.27 (0.31), residues: 769
  helix:  1.22 (0.28), residues: 369
  sheet: -2.19 (0.56), residues: 81
  loop : -3.10 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 347 
 TYR   0.012   0.001   TYR A 338 
 PHE   0.013   0.001   PHE A 337 
 TRP   0.014   0.001   TRP A 935 
 HIS   0.006   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 5980)
  covalent geometry    : angle       0.84949 ( 8124)
  hydrogen bonds       : bond        0.12936 (  291)
  hydrogen bonds       : angle       5.86357 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 PHE cc_start: 0.9086 (m-10) cc_final: 0.8883 (m-10)
REVERT: A  387 GLU cc_start: 0.8275 (mp0) cc_final: 0.8031 (mp0)
REVERT: A  526 GLU cc_start: 0.8796 (pm20) cc_final: 0.8555 (pm20)
REVERT: A  630 GLU cc_start: 0.8610 (mp0) cc_final: 0.8246 (mp0)
REVERT: A  647 THR cc_start: 0.7809 (p) cc_final: 0.7269 (p)
REVERT: A  659 PHE cc_start: 0.9502 (p90) cc_final: 0.9236 (p90)
REVERT: A  881 MET cc_start: 0.9033 (tpp) cc_final: 0.8789 (mmm)
REVERT: A  887 ASP cc_start: 0.8728 (m-30) cc_final: 0.8449 (m-30)
REVERT: A  915 LEU cc_start: 0.9216 (mt) cc_final: 0.9009 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0725
  time to fit residues: 10.8853
Evaluate side-chains
  64 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 270 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.123656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.081033 restraints weight = 17214.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 4.97
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086   5980  Z= 0.207
  Angle     :  0.771  10.325   8124  Z= 0.392
  Chirality :  0.048   0.208    963
  Planarity :  0.006   0.050   1027
  Dihedral  :  5.656  29.607    818
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 12.61 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 10.02 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.14 (0.31), residues: 769
  helix:  1.15 (0.28), residues: 374
  sheet: -1.66 (0.63), residues: 66
  loop : -2.97 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 896 
 TYR   0.013   0.001   TYR A 689 
 PHE   0.015   0.001   PHE A 337 
 TRP   0.020   0.002   TRP A 935 
 HIS   0.003   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 5980)
  covalent geometry    : angle       0.77072 ( 8124)
  hydrogen bonds       : bond        0.04288 (  291)
  hydrogen bonds       : angle       5.41622 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8618 (mtm)
REVERT: A  630 GLU cc_start: 0.8612 (mp0) cc_final: 0.8176 (mp0)
REVERT: A  659 PHE cc_start: 0.9500 (p90) cc_final: 0.9230 (p90)
REVERT: A  887 ASP cc_start: 0.8692 (m-30) cc_final: 0.8369 (m-30)
  outliers start: 18
  outliers final: 11
  residues processed: 84
  average time/residue: 0.0735
  time to fit residues: 8.5050
Evaluate side-chains
  71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 270 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.123849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.080656 restraints weight = 17084.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 5.25
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5980  Z= 0.163
  Angle     :  0.743  10.915   8124  Z= 0.372
  Chirality :  0.047   0.221    963
  Planarity :  0.005   0.051   1027
  Dihedral  :  5.616  29.030    818
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 12.22 %
    Favored  : 87.26 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.46 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.02 (0.31), residues: 769
  helix:  1.23 (0.28), residues: 374
  sheet: -1.51 (0.64), residues: 66
  loop : -2.91 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 896 
 TYR   0.009   0.001   TYR A 338 
 PHE   0.014   0.001   PHE A 337 
 TRP   0.017   0.001   TRP A 935 
 HIS   0.003   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5980)
  covalent geometry    : angle       0.74262 ( 8124)
  hydrogen bonds       : bond        0.03741 (  291)
  hydrogen bonds       : angle       5.19905 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.8827 (ttm) cc_final: 0.8310 (mtp)
REVERT: A  361 ASN cc_start: 0.8706 (t0) cc_final: 0.8289 (m-40)
REVERT: A  375 LEU cc_start: 0.9599 (tp) cc_final: 0.9299 (tp)
REVERT: A  659 PHE cc_start: 0.9499 (p90) cc_final: 0.9182 (p90)
REVERT: A  887 ASP cc_start: 0.8750 (m-30) cc_final: 0.8359 (m-30)
REVERT: A  924 LEU cc_start: 0.9418 (mt) cc_final: 0.9061 (tt)
  outliers start: 20
  outliers final: 12
  residues processed: 81
  average time/residue: 0.0688
  time to fit residues: 7.8183
Evaluate side-chains
  77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 12 optimal weight:    0.4980
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.120773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.077407 restraints weight = 17281.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 5.00
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   5980  Z= 0.260
  Angle     :  0.793  10.840   8124  Z= 0.400
  Chirality :  0.048   0.209    963
  Planarity :  0.005   0.049   1027
  Dihedral  :  5.700  30.560    818
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 12.35 %
    Favored  : 87.26 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.71 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.02 (0.31), residues: 769
  helix:  1.09 (0.27), residues: 374
  sheet: -0.63 (0.76), residues: 55
  loop : -2.88 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 269 
 TYR   0.015   0.001   TYR A 689 
 PHE   0.019   0.002   PHE A 562 
 TRP   0.022   0.002   TRP A 935 
 HIS   0.004   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 5980)
  covalent geometry    : angle       0.79281 ( 8124)
  hydrogen bonds       : bond        0.04058 (  291)
  hydrogen bonds       : angle       5.39923 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 GLU cc_start: 0.8306 (mp0) cc_final: 0.7933 (mp0)
REVERT: A  630 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8205 (mp0)
REVERT: A  659 PHE cc_start: 0.9538 (p90) cc_final: 0.9201 (p90)
REVERT: A  881 MET cc_start: 0.9114 (mmm) cc_final: 0.8804 (mmm)
REVERT: A  887 ASP cc_start: 0.8804 (m-30) cc_final: 0.8394 (m-30)
REVERT: A  924 LEU cc_start: 0.9472 (mt) cc_final: 0.9133 (tt)
  outliers start: 21
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0757
  time to fit residues: 8.2564
Evaluate side-chains
  79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.123771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.082047 restraints weight = 17475.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 4.78
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5980  Z= 0.140
  Angle     :  0.756  12.060   8124  Z= 0.367
  Chirality :  0.046   0.211    963
  Planarity :  0.005   0.058   1027
  Dihedral  :  5.609  30.189    818
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 11.44 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.84 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.82 (0.31), residues: 769
  helix:  1.35 (0.28), residues: 374
  sheet: -1.30 (0.65), residues: 64
  loop : -2.78 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 694 
 TYR   0.008   0.001   TYR A 366 
 PHE   0.012   0.001   PHE A 337 
 TRP   0.010   0.001   TRP A 935 
 HIS   0.005   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5980)
  covalent geometry    : angle       0.75566 ( 8124)
  hydrogen bonds       : bond        0.03422 (  291)
  hydrogen bonds       : angle       5.12948 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8839 (mtm) cc_final: 0.8621 (mtm)
REVERT: A  361 ASN cc_start: 0.8664 (t0) cc_final: 0.8417 (m-40)
REVERT: A  630 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8154 (mp0)
REVERT: A  659 PHE cc_start: 0.9472 (p90) cc_final: 0.9105 (p90)
REVERT: A  881 MET cc_start: 0.9099 (mmm) cc_final: 0.8817 (mmm)
REVERT: A  887 ASP cc_start: 0.8752 (m-30) cc_final: 0.8516 (m-30)
REVERT: A  924 LEU cc_start: 0.9412 (mt) cc_final: 0.9078 (tt)
  outliers start: 17
  outliers final: 14
  residues processed: 83
  average time/residue: 0.0776
  time to fit residues: 8.8793
Evaluate side-chains
  75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 58 optimal weight:   30.0000
   chunk 48 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.123518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.080969 restraints weight = 17303.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 4.75
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5980  Z= 0.154
  Angle     :  0.730  10.708   8124  Z= 0.365
  Chirality :  0.046   0.204    963
  Planarity :  0.005   0.055   1027
  Dihedral  :  5.494  29.626    818
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 12.35 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.68 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.77 (0.31), residues: 769
  helix:  1.46 (0.27), residues: 374
  sheet: -1.23 (0.67), residues: 60
  loop : -2.84 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 694 
 TYR   0.016   0.001   TYR A 689 
 PHE   0.016   0.001   PHE A 562 
 TRP   0.012   0.001   TRP A 935 
 HIS   0.003   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5980)
  covalent geometry    : angle       0.72980 ( 8124)
  hydrogen bonds       : bond        0.03468 (  291)
  hydrogen bonds       : angle       5.10467 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.8781 (ttm) cc_final: 0.8485 (mtp)
REVERT: A  387 GLU cc_start: 0.8192 (mp0) cc_final: 0.7954 (mp0)
REVERT: A  630 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8193 (mp0)
REVERT: A  659 PHE cc_start: 0.9545 (p90) cc_final: 0.9100 (p90)
REVERT: A  750 MET cc_start: 0.9235 (tpt) cc_final: 0.8977 (tpt)
REVERT: A  881 MET cc_start: 0.9114 (mmm) cc_final: 0.8800 (mmm)
REVERT: A  887 ASP cc_start: 0.8724 (m-30) cc_final: 0.8292 (m-30)
REVERT: A  924 LEU cc_start: 0.9426 (mt) cc_final: 0.9102 (tt)
  outliers start: 19
  outliers final: 16
  residues processed: 82
  average time/residue: 0.0759
  time to fit residues: 8.5887
Evaluate side-chains
  81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  914 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.123307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.080823 restraints weight = 17309.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 4.78
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5980  Z= 0.152
  Angle     :  0.752  12.679   8124  Z= 0.371
  Chirality :  0.046   0.203    963
  Planarity :  0.005   0.053   1027
  Dihedral  :  5.477  29.691    818
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 11.44 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.15 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.71 (0.31), residues: 769
  helix:  1.53 (0.27), residues: 375
  sheet: -1.25 (0.67), residues: 59
  loop : -2.85 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 694 
 TYR   0.007   0.001   TYR A 366 
 PHE   0.012   0.001   PHE A 337 
 TRP   0.011   0.001   TRP A 935 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5980)
  covalent geometry    : angle       0.75152 ( 8124)
  hydrogen bonds       : bond        0.03405 (  291)
  hydrogen bonds       : angle       5.05012 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 ASN cc_start: 0.8744 (t0) cc_final: 0.8427 (m-40)
REVERT: A  387 GLU cc_start: 0.8251 (mp0) cc_final: 0.7967 (mp0)
REVERT: A  630 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8188 (mp0)
REVERT: A  659 PHE cc_start: 0.9577 (p90) cc_final: 0.9088 (p90)
REVERT: A  680 HIS cc_start: 0.7439 (m170) cc_final: 0.7236 (m90)
REVERT: A  750 MET cc_start: 0.9224 (tpt) cc_final: 0.8961 (tpt)
REVERT: A  881 MET cc_start: 0.9119 (mmm) cc_final: 0.8814 (mmm)
REVERT: A  887 ASP cc_start: 0.8716 (m-30) cc_final: 0.8295 (m-30)
REVERT: A  924 LEU cc_start: 0.9427 (mt) cc_final: 0.9112 (tt)
  outliers start: 17
  outliers final: 15
  residues processed: 78
  average time/residue: 0.0743
  time to fit residues: 8.0214
Evaluate side-chains
  78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 52 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 70 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.122630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.080362 restraints weight = 17208.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 5.02
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5980  Z= 0.149
  Angle     :  0.738  10.966   8124  Z= 0.366
  Chirality :  0.047   0.197    963
  Planarity :  0.005   0.053   1027
  Dihedral  :  5.421  29.016    818
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 11.83 %
    Favored  : 87.91 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.00 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.66 (0.31), residues: 769
  helix:  1.58 (0.28), residues: 375
  sheet: -1.25 (0.68), residues: 57
  loop : -2.82 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 694 
 TYR   0.020   0.001   TYR A 689 
 PHE   0.021   0.001   PHE A 562 
 TRP   0.011   0.001   TRP A 935 
 HIS   0.003   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5980)
  covalent geometry    : angle       0.73813 ( 8124)
  hydrogen bonds       : bond        0.03332 (  291)
  hydrogen bonds       : angle       5.02022 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 ASN cc_start: 0.8698 (t0) cc_final: 0.8363 (m-40)
REVERT: A  630 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8191 (mp0)
REVERT: A  659 PHE cc_start: 0.9626 (p90) cc_final: 0.9128 (p90)
REVERT: A  750 MET cc_start: 0.9199 (tpt) cc_final: 0.8931 (tpt)
REVERT: A  881 MET cc_start: 0.9122 (mmm) cc_final: 0.8816 (mmm)
REVERT: A  887 ASP cc_start: 0.8718 (m-30) cc_final: 0.8307 (m-30)
REVERT: A  924 LEU cc_start: 0.9408 (mt) cc_final: 0.9101 (tt)
  outliers start: 21
  outliers final: 18
  residues processed: 81
  average time/residue: 0.0694
  time to fit residues: 7.7945
Evaluate side-chains
  84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 HIS
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  914 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0980
   chunk 3 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.123679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.081776 restraints weight = 17296.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 4.92
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5980  Z= 0.135
  Angle     :  0.754  10.695   8124  Z= 0.369
  Chirality :  0.047   0.217    963
  Planarity :  0.005   0.054   1027
  Dihedral  :  5.459  29.013    818
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.70 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.78 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.61 (0.31), residues: 769
  helix:  1.62 (0.28), residues: 375
  sheet: -1.57 (0.68), residues: 42
  loop : -2.70 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 274 
 TYR   0.007   0.001   TYR A 689 
 PHE   0.011   0.001   PHE A 337 
 TRP   0.009   0.001   TRP A 935 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5980)
  covalent geometry    : angle       0.75369 ( 8124)
  hydrogen bonds       : bond        0.03289 (  291)
  hydrogen bonds       : angle       4.94497 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.8410 (mtp) cc_final: 0.8208 (mtp)
REVERT: A  319 MET cc_start: 0.8763 (ptp) cc_final: 0.8558 (ptp)
REVERT: A  361 ASN cc_start: 0.8626 (t0) cc_final: 0.8328 (m-40)
REVERT: A  630 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8164 (mp0)
REVERT: A  659 PHE cc_start: 0.9556 (p90) cc_final: 0.9046 (p90)
REVERT: A  750 MET cc_start: 0.9217 (tpt) cc_final: 0.8943 (tpt)
REVERT: A  881 MET cc_start: 0.9111 (mmm) cc_final: 0.8798 (mmm)
REVERT: A  887 ASP cc_start: 0.8714 (m-30) cc_final: 0.8294 (m-30)
  outliers start: 16
  outliers final: 16
  residues processed: 76
  average time/residue: 0.0639
  time to fit residues: 6.9778
Evaluate side-chains
  80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 HIS
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0060
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   chunk 9 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.122684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.080298 restraints weight = 17293.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 5.02
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5980  Z= 0.159
  Angle     :  0.757  10.466   8124  Z= 0.374
  Chirality :  0.047   0.203    963
  Planarity :  0.005   0.055   1027
  Dihedral  :  5.462  28.962    818
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 12.35 %
    Favored  : 87.52 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.72 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.59 (0.32), residues: 769
  helix:  1.62 (0.28), residues: 375
  sheet: -1.13 (0.67), residues: 56
  loop : -2.77 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 274 
 TYR   0.025   0.001   TYR A 689 
 PHE   0.028   0.001   PHE A 562 
 TRP   0.012   0.001   TRP A 935 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5980)
  covalent geometry    : angle       0.75722 ( 8124)
  hydrogen bonds       : bond        0.03382 (  291)
  hydrogen bonds       : angle       4.97137 (  834)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8775 (ptp) cc_final: 0.8545 (ptp)
REVERT: A  630 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8179 (mp0)
REVERT: A  659 PHE cc_start: 0.9608 (p90) cc_final: 0.9114 (p90)
REVERT: A  750 MET cc_start: 0.9275 (tpt) cc_final: 0.9024 (tpt)
REVERT: A  881 MET cc_start: 0.9125 (mmm) cc_final: 0.8800 (mmm)
REVERT: A  887 ASP cc_start: 0.8717 (m-30) cc_final: 0.8300 (m-30)
REVERT: A  924 LEU cc_start: 0.9437 (mt) cc_final: 0.9039 (pt)
  outliers start: 15
  outliers final: 15
  residues processed: 72
  average time/residue: 0.0793
  time to fit residues: 7.7921
Evaluate side-chains
  77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 71 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0770
   chunk 72 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.124134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.082200 restraints weight = 17050.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 4.91
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5980  Z= 0.127
  Angle     :  0.754  10.655   8124  Z= 0.368
  Chirality :  0.047   0.201    963
  Planarity :  0.005   0.054   1027
  Dihedral  :  5.429  28.917    818
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.70 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.19 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.52 (0.32), residues: 769
  helix:  1.68 (0.28), residues: 375
  sheet: -1.53 (0.69), residues: 42
  loop : -2.62 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 274 
 TYR   0.007   0.001   TYR A 689 
 PHE   0.024   0.001   PHE A 562 
 TRP   0.007   0.001   TRP A 935 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5980)
  covalent geometry    : angle       0.75444 ( 8124)
  hydrogen bonds       : bond        0.03265 (  291)
  hydrogen bonds       : angle       4.87198 (  834)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1551.51 seconds
wall clock time: 27 minutes 30.38 seconds (1650.38 seconds total)