Starting phenix.real_space_refine
on Thu Jul 24 10:25:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dqk_27655/07_2025/8dqk_27655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dqk_27655/07_2025/8dqk_27655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dqk_27655/07_2025/8dqk_27655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dqk_27655/07_2025/8dqk_27655.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dqk_27655/07_2025/8dqk_27655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dqk_27655/07_2025/8dqk_27655.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      21      5.16       5
     C    3844      2.51       5
     N    1002      2.21       5
     O    1024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5891
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 733, 5891
          Classifications: {'peptide': 733}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 691}
          Chain breaks: 3
  Time building chain proxies: 7.76, per 1000 atoms: 1.32
  Number of scatterers: 5891
  At special positions: 0
  Unit cell: (83.83, 84.66, 107.9, 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      21     16.00
     O    1024      8.00
     N    1002      7.00
     C    3844      6.00
    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: 1.63
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1374

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      60.7% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 129
      Proline residue:  A 107  - end of helix
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 157
    Processing helix  chain 'A' and resid 158 through 160
      No H-bonds generated for 'chain 'A' and resid 158 through 160'
    Processing helix  chain 'A' and resid 169 through 176
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.548A  pdb=" N   THR A 205 " --> pdb=" O   PRO A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 257
      removed outlier: 4.087A  pdb=" N   THR A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   LEU A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
      Proline residue:  A 251  - end of helix
    Processing helix  chain 'A' and resid 262 through 268
    Processing helix  chain 'A' and resid 279 through 302
    Processing helix  chain 'A' and resid 302 through 316
    Processing helix  chain 'A' and resid 405 through 422
      removed outlier: 3.720A  pdb=" N   LEU A 420 " --> pdb=" O   ARG A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 4.485A  pdb=" N   PHE A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 484
    Processing helix  chain 'A' and resid 486 through 491
    Processing helix  chain 'A' and resid 579 through 585
      removed outlier: 3.590A  pdb=" N   ALA A 583 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 592
      removed outlier: 4.054A  pdb=" N   ALA A 590 " --> pdb=" O   SER A 587 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 592 " --> pdb=" O   TYR A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 610
    Processing helix  chain 'A' and resid 611 through 616
      removed outlier: 3.912A  pdb=" N   PHE A 614 " --> pdb=" O   ALA A 611 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS A 616 " --> pdb=" O   ALA A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 643
      removed outlier: 4.219A  pdb=" N   VAL A 636 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 686
    Processing helix  chain 'A' and resid 689 through 693
    Processing helix  chain 'A' and resid 698 through 711
    Processing helix  chain 'A' and resid 713 through 732
      removed outlier: 4.366A  pdb=" N   PHE A 717 " --> pdb=" O   PHE A 713 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   PHE A 720 " --> pdb=" O   ILE A 716 " (cutoff:3.500A)
      Proline residue:  A 725  - end of helix
    Processing helix  chain 'A' and resid 740 through 765
    Processing helix  chain 'A' and resid 768 through 800
      removed outlier: 4.159A  pdb=" N   TYR A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   LEU A 788 " --> pdb=" O   CYS A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
      removed outlier: 3.666A  pdb=" N   VAL A 827 " --> pdb=" O   ASP A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 833
      No H-bonds generated for 'chain 'A' and resid 831 through 833'
    Processing helix  chain 'A' and resid 834 through 857
      removed outlier: 4.041A  pdb=" N   ILE A 838 " --> pdb=" O   MET A 834 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE A 839 " --> pdb=" O   ILE A 835 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE A 840 " --> pdb=" O   THR A 836 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN A 844 " --> pdb=" O   ILE A 840 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A 849 " --> pdb=" O   ILE A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 867
    Processing helix  chain 'A' and resid 868 through 889
      Proline residue:  A 882  - end of helix
      removed outlier: 4.404A  pdb=" N   LEU A 888 " --> pdb=" O   ALA A 884 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLY A 889 " --> pdb=" O   LYS A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 893
    Processing helix  chain 'A' and resid 894 through 916
      removed outlier: 4.618A  pdb=" N   VAL A 898 " --> pdb=" O   THR A 894 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL A 900 " --> pdb=" O   VAL A 896 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 99
    Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 360
      removed outlier: 6.507A  pdb=" N   LEU A 391 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 8.752A  pdb=" N   VAL A 392 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   CYS A 224 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL A 394 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL A 226 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   ASP A 189 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   LEU A 430 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   PHE A 191 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   CYS A 503 " --> pdb=" O   ASN A 429 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ALA A 458 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   ARG A 649 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   VAL A 460 " --> pdb=" O   ARG A 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 436
      removed outlier: 6.404A  pdb=" N   ARG A 465 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    903 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: 2.81

  Time building geometry restraints manager: 2.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1858
        1.34 -     1.46: 1547
        1.46 -     1.58: 2631
        1.58 -     1.70: 0
        1.70 -     1.81: 33
  Bond restraints: 6069
  Sorted by residual:
  bond pdb=" CA  ARG A 348 "
       pdb=" CB  ARG A 348 "
    ideal  model  delta    sigma   weight residual
    1.529  1.560 -0.031 1.66e-02 3.63e+03 3.57e+00
  bond pdb=" CB  GLU A 668 "
       pdb=" CG  GLU A 668 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 3.00e-02 1.11e+03 2.61e+00
  bond pdb=" N   LYS A 406 "
       pdb=" CA  LYS A 406 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.019 1.29e-02 6.01e+03 2.19e+00
  bond pdb=" C   TYR A 881 "
       pdb=" N   PRO A 882 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.09e+00
  bond pdb=" CB  ASN A 161 "
       pdb=" CG  ASN A 161 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.88e-01
  ... (remaining 6064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 8016
        1.80 -     3.61: 208
        3.61 -     5.41: 42
        5.41 -     7.21: 11
        7.21 -     9.01: 2
  Bond angle restraints: 8279
  Sorted by residual:
  angle pdb=" N   VAL A 866 "
        pdb=" CA  VAL A 866 "
        pdb=" C   VAL A 866 "
      ideal   model   delta    sigma   weight residual
     112.83  106.74    6.09 9.90e-01 1.02e+00 3.78e+01
  angle pdb=" C   ILE A 664 "
        pdb=" N   ASN A 665 "
        pdb=" CA  ASN A 665 "
      ideal   model   delta    sigma   weight residual
     121.54  128.24   -6.70 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" N   GLN A 279 "
        pdb=" CA  GLN A 279 "
        pdb=" C   GLN A 279 "
      ideal   model   delta    sigma   weight residual
     112.12  108.00    4.12 1.34e+00 5.57e-01 9.47e+00
  angle pdb=" CA  ARG A 675 "
        pdb=" CB  ARG A 675 "
        pdb=" CG  ARG A 675 "
      ideal   model   delta    sigma   weight residual
     114.10  119.97   -5.87 2.00e+00 2.50e-01 8.63e+00
  angle pdb=" C   VAL A 609 "
        pdb=" CA  VAL A 609 "
        pdb=" CB  VAL A 609 "
      ideal   model   delta    sigma   weight residual
     111.88  107.99    3.89 1.37e+00 5.33e-01 8.05e+00
  ... (remaining 8274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3222
       17.97 -    35.93: 253
       35.93 -    53.90: 25
       53.90 -    71.86: 7
       71.86 -    89.83: 3
  Dihedral angle restraints: 3510
    sinusoidal: 1379
      harmonic: 2131
  Sorted by residual:
  dihedral pdb=" CA  TRP A 863 "
           pdb=" C   TRP A 863 "
           pdb=" N   LEU A 864 "
           pdb=" CA  LEU A 864 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.85  -28.15     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  GLN A 405 "
           pdb=" C   GLN A 405 "
           pdb=" N   LYS A 406 "
           pdb=" CA  LYS A 406 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.95   18.05     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ILE A 841 "
           pdb=" C   ILE A 841 "
           pdb=" N   PHE A 842 "
           pdb=" CA  PHE A 842 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.17  -16.83     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 3507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 663
       0.044 -    0.088: 188
       0.088 -    0.132: 55
       0.132 -    0.176: 8
       0.176 -    0.220: 3
  Chirality restraints: 917
  Sorted by residual:
  chirality pdb=" CB  ILE A 427 "
            pdb=" CA  ILE A 427 "
            pdb=" CG1 ILE A 427 "
            pdb=" CG2 ILE A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ASN A 665 "
            pdb=" N   ASN A 665 "
            pdb=" C   ASN A 665 "
            pdb=" CB  ASN A 665 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CB  ILE A 624 "
            pdb=" CA  ILE A 624 "
            pdb=" CG1 ILE A 624 "
            pdb=" CG2 ILE A 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  ... (remaining 914 not shown)

  Planarity restraints: 1043
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 217 "   -0.035 5.00e-02 4.00e+02   5.24e-02 4.39e+00
        pdb=" N   PRO A 218 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 218 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 218 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 166 "    0.033 5.00e-02 4.00e+02   5.06e-02 4.10e+00
        pdb=" N   PRO A 167 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 167 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 167 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 779 "   -0.012 2.00e-02 2.50e+03   1.09e-02 2.97e+00
        pdb=" CG  TRP A 779 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 779 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 779 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 779 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 779 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 779 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1040 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 100
        2.69 -     3.24: 6008
        3.24 -     3.79: 9288
        3.79 -     4.35: 11698
        4.35 -     4.90: 18853
  Nonbonded interactions: 45947
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 361 "
            pdb=" N   HIS A 362 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" NE2 GLN A 777 "
            pdb=" O   PHE A 878 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" O   ALA A 606 "
            pdb=" OG1 THR A 610 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" N   ILE A 664 "
            pdb=" OE2 GLU A 668 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   ALA A 240 "
            pdb=" OG  SER A 243 "
     model   vdw
     2.318 3.040
  ... (remaining 45942 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:             3.060
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     27.830
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:4.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5812
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      :  0.003   0.049   6069  Z= 0.144
  Angle     :  0.720   9.014   8279  Z= 0.398
  Chirality :  0.045   0.220    917
  Planarity :  0.005   0.052   1043
  Dihedral  : 12.564  89.826   2136
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.62 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.32), residues: 725
  helix:  0.74 (0.27), residues: 392
  sheet: -0.64 (0.58), residues: 72
  loop : -0.53 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 779 
 HIS   0.005   0.001   HIS A 879 
 PHE   0.022   0.002   PHE A 773 
 TYR   0.029   0.002   TYR A 696 
 ARG   0.004   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09896 (  312)
  hydrogen bonds       : angle       4.22912 (  903)
  covalent geometry    : bond        0.00286 ( 6069)
  covalent geometry    : angle       0.72047 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4370 (tpp) cc_final: 0.4125 (tpp)
REVERT: A  308 LYS cc_start: 0.8552 (pptt) cc_final: 0.8210 (pptt)
REVERT: A  493 MET cc_start: 0.4007 (ppp) cc_final: 0.2897 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2036
  time to fit residues: 21.6962
Evaluate side-chains
  49 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 GLN
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 402 HIS
A 478 HIS
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.082376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.074674 restraints weight = 38995.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.075825 restraints weight = 28156.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.076709 restraints weight = 21327.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6069  Z= 0.293
  Angle     :  0.856   8.671   8279  Z= 0.457
  Chirality :  0.051   0.248    917
  Planarity :  0.008   0.069   1043
  Dihedral  :  5.317  22.667    802
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 21.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.72 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.06 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.30), residues: 725
  helix: -0.33 (0.25), residues: 389
  sheet: -0.13 (0.63), residues: 69
  loop : -1.16 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 779 
 HIS   0.008   0.002   HIS A 272 
 PHE   0.036   0.004   PHE A 267 
 TYR   0.024   0.003   TYR A 393 
 ARG   0.008   0.001   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05192 (  312)
  hydrogen bonds       : angle       5.22810 (  903)
  covalent geometry    : bond        0.00620 ( 6069)
  covalent geometry    : angle       0.85626 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4572 (tpp) cc_final: 0.4231 (tpp)
REVERT: A  212 ILE cc_start: 0.9202 (pt) cc_final: 0.8902 (mt)
REVERT: A  309 GLN cc_start: 0.9083 (mm110) cc_final: 0.8858 (mm110)
REVERT: A  411 MET cc_start: 0.8759 (ptm) cc_final: 0.8422 (ptm)
REVERT: A  773 PHE cc_start: 0.8039 (t80) cc_final: 0.7614 (t80)
  outliers start: 16
  outliers final: 9
  residues processed: 73
  average time/residue: 0.1913
  time to fit residues: 19.2721
Evaluate side-chains
  51 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  314 TYR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  887 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 352 HIS
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 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 = 0.3982 r_free = 0.3982 target = 0.081661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.073865 restraints weight = 39661.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.075058 restraints weight = 27971.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.075884 restraints weight = 21267.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6069  Z= 0.189
  Angle     :  0.648   8.328   8279  Z= 0.338
  Chirality :  0.043   0.149    917
  Planarity :  0.005   0.050   1043
  Dihedral  :  4.676  19.271    802
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.31 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 11.76 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.31), residues: 725
  helix:  0.29 (0.26), residues: 387
  sheet: -0.04 (0.66), residues: 66
  loop : -0.82 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 779 
 HIS   0.005   0.001   HIS A 272 
 PHE   0.031   0.002   PHE A 614 
 TYR   0.021   0.002   TYR A 654 
 ARG   0.004   0.001   ARG A 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  312)
  hydrogen bonds       : angle       4.68831 (  903)
  covalent geometry    : bond        0.00412 ( 6069)
  covalent geometry    : angle       0.64807 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 50
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4536 (tpp) cc_final: 0.4178 (tpp)
REVERT: A  193 THR cc_start: 0.9181 (m) cc_final: 0.8937 (p)
REVERT: A  773 PHE cc_start: 0.8091 (t80) cc_final: 0.7651 (t80)
REVERT: A  826 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6137 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 64
  average time/residue: 0.2700
  time to fit residues: 24.3679
Evaluate side-chains
  56 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  745 VAL
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  900 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 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 = 0.3966 r_free = 0.3966 target = 0.080751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.072833 restraints weight = 39722.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.074066 restraints weight = 27764.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.074889 restraints weight = 20908.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.5428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6069  Z= 0.154
  Angle     :  0.597   6.192   8279  Z= 0.312
  Chirality :  0.042   0.147    917
  Planarity :  0.005   0.045   1043
  Dihedral  :  4.522  18.041    802
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.72 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 12.56 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.32), residues: 725
  helix:  0.49 (0.27), residues: 385
  sheet:  0.04 (0.66), residues: 64
  loop : -0.74 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 779 
 HIS   0.005   0.001   HIS A 305 
 PHE   0.027   0.002   PHE A 614 
 TYR   0.014   0.002   TYR A 274 
 ARG   0.004   0.001   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03695 (  312)
  hydrogen bonds       : angle       4.56163 (  903)
  covalent geometry    : bond        0.00339 ( 6069)
  covalent geometry    : angle       0.59701 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4528 (tpp) cc_final: 0.4232 (tpp)
REVERT: A  193 THR cc_start: 0.9183 (m) cc_final: 0.8978 (p)
REVERT: A  212 ILE cc_start: 0.9239 (pt) cc_final: 0.8824 (mt)
REVERT: A  773 PHE cc_start: 0.8081 (t80) cc_final: 0.7626 (t80)
REVERT: A  826 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.6067 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 65
  average time/residue: 0.1570
  time to fit residues: 14.8745
Evaluate side-chains
  62 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  900 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0040
   chunk 48 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 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 = 0.3995 r_free = 0.3995 target = 0.082564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.074583 restraints weight = 38849.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.075784 restraints weight = 27718.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.076603 restraints weight = 21319.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6069  Z= 0.113
  Angle     :  0.561   5.955   8279  Z= 0.288
  Chirality :  0.041   0.143    917
  Planarity :  0.005   0.042   1043
  Dihedral  :  4.236  16.589    802
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.59 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.47 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.32), residues: 725
  helix:  0.82 (0.27), residues: 390
  sheet:  0.14 (0.68), residues: 59
  loop : -0.64 (0.40), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 764 
 HIS   0.002   0.001   HIS A 305 
 PHE   0.021   0.001   PHE A 614 
 TYR   0.013   0.001   TYR A 881 
 ARG   0.002   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03362 (  312)
  hydrogen bonds       : angle       4.28025 (  903)
  covalent geometry    : bond        0.00252 ( 6069)
  covalent geometry    : angle       0.56138 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4477 (tpp) cc_final: 0.4113 (tpp)
REVERT: A  773 PHE cc_start: 0.8075 (t80) cc_final: 0.7593 (t80)
REVERT: A  826 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.5792 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 67
  average time/residue: 0.1356
  time to fit residues: 13.2018
Evaluate side-chains
  58 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0870
   chunk 8 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    2.7964

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.078854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.071134 restraints weight = 39869.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.072338 restraints weight = 27895.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.073137 restraints weight = 21076.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.6226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6069  Z= 0.172
  Angle     :  0.625   6.566   8279  Z= 0.325
  Chirality :  0.042   0.143    917
  Planarity :  0.005   0.042   1043
  Dihedral  :  4.456  18.100    802
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 15.74 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.32), residues: 725
  helix:  0.70 (0.27), residues: 390
  sheet: -0.17 (0.64), residues: 66
  loop : -0.73 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 902 
 HIS   0.003   0.001   HIS A 402 
 PHE   0.027   0.002   PHE A 614 
 TYR   0.014   0.002   TYR A 393 
 ARG   0.003   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  312)
  hydrogen bonds       : angle       4.62722 (  903)
  covalent geometry    : bond        0.00376 ( 6069)
  covalent geometry    : angle       0.62530 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 51
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4618 (tpp) cc_final: 0.4357 (tpp)
REVERT: A  403 ASP cc_start: 0.8371 (p0) cc_final: 0.8133 (t0)
REVERT: A  773 PHE cc_start: 0.8124 (t80) cc_final: 0.7604 (t80)
REVERT: A  826 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.5903 (m-80)
  outliers start: 22
  outliers final: 14
  residues processed: 68
  average time/residue: 0.1551
  time to fit residues: 14.8678
Evaluate side-chains
  64 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 59 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 106 HIS
** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.074036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.066479 restraints weight = 40515.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.067593 restraints weight = 28521.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.068382 restraints weight = 21678.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.7693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   6069  Z= 0.299
  Angle     :  0.812   8.779   8279  Z= 0.428
  Chirality :  0.047   0.151    917
  Planarity :  0.007   0.059   1043
  Dihedral  :  5.295  22.790    802
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 21.83
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.24 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 18.28 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.31), residues: 725
  helix: -0.04 (0.26), residues: 387
  sheet: -0.20 (0.67), residues: 60
  loop : -1.11 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 779 
 HIS   0.007   0.002   HIS A 698 
 PHE   0.039   0.003   PHE A 614 
 TYR   0.021   0.003   TYR A 393 
 ARG   0.010   0.001   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04955 (  312)
  hydrogen bonds       : angle       5.57057 (  903)
  covalent geometry    : bond        0.00622 ( 6069)
  covalent geometry    : angle       0.81152 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  109 ARG cc_start: 0.3986 (OUTLIER) cc_final: 0.3703 (ptt180)
REVERT: A  308 LYS cc_start: 0.9315 (pptt) cc_final: 0.8886 (tptp)
REVERT: A  773 PHE cc_start: 0.8317 (t80) cc_final: 0.7794 (t80)
REVERT: A  826 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6370 (m-80)
  outliers start: 23
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1825
  time to fit residues: 18.2750
Evaluate side-chains
  68 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  579 THR
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0170
   chunk 57 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    2.0424

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.075965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.068419 restraints weight = 39287.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.069597 restraints weight = 27065.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.070378 restraints weight = 20204.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.7792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6069  Z= 0.154
  Angle     :  0.689   8.684   8279  Z= 0.352
  Chirality :  0.044   0.141    917
  Planarity :  0.005   0.045   1043
  Dihedral  :  4.896  18.609    802
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.00 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.46 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.31), residues: 725
  helix:  0.33 (0.26), residues: 391
  sheet: -0.16 (0.67), residues: 59
  loop : -0.96 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 764 
 HIS   0.005   0.001   HIS A 698 
 PHE   0.029   0.002   PHE A 614 
 TYR   0.019   0.002   TYR A 293 
 ARG   0.004   0.001   ARG A 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  312)
  hydrogen bonds       : angle       4.87471 (  903)
  covalent geometry    : bond        0.00342 ( 6069)
  covalent geometry    : angle       0.68883 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ARG cc_start: 0.3939 (OUTLIER) cc_final: 0.3620 (ptt180)
REVERT: A  135 MET cc_start: 0.6352 (tmm) cc_final: 0.4429 (tpp)
REVERT: A  308 LYS cc_start: 0.9257 (pptt) cc_final: 0.8828 (tptp)
REVERT: A  390 MET cc_start: 0.7302 (mmm) cc_final: 0.6694 (mmm)
REVERT: A  773 PHE cc_start: 0.8279 (t80) cc_final: 0.7722 (t80)
REVERT: A  826 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6259 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 65
  average time/residue: 0.1903
  time to fit residues: 16.5542
Evaluate side-chains
  64 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 38 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0050
   chunk 31 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.8002

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 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 = 0.3903 r_free = 0.3903 target = 0.077800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.070322 restraints weight = 39057.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.071496 restraints weight = 26819.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.072325 restraints weight = 20016.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.7661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6069  Z= 0.128
  Angle     :  0.658   8.931   8279  Z= 0.334
  Chirality :  0.043   0.153    917
  Planarity :  0.005   0.047   1043
  Dihedral  :  4.500  16.218    802
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.14 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.94 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.31), residues: 725
  helix:  0.64 (0.27), residues: 382
  sheet: -0.03 (0.69), residues: 54
  loop : -0.95 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 764 
 HIS   0.004   0.001   HIS A 698 
 PHE   0.016   0.002   PHE A 614 
 TYR   0.025   0.002   TYR A 746 
 ARG   0.005   0.000   ARG A 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  312)
  hydrogen bonds       : angle       4.55791 (  903)
  covalent geometry    : bond        0.00287 ( 6069)
  covalent geometry    : angle       0.65796 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 ARG cc_start: 0.4028 (OUTLIER) cc_final: 0.3743 (ptt180)
REVERT: A  135 MET cc_start: 0.6182 (tmm) cc_final: 0.4492 (ttm)
REVERT: A  308 LYS cc_start: 0.9174 (pptt) cc_final: 0.8601 (tppt)
REVERT: A  390 MET cc_start: 0.7255 (mmm) cc_final: 0.6666 (mmm)
REVERT: A  668 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7596 (pm20)
REVERT: A  773 PHE cc_start: 0.8159 (t80) cc_final: 0.7699 (t80)
REVERT: A  826 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6082 (m-80)
REVERT: A  864 LEU cc_start: 0.2309 (OUTLIER) cc_final: 0.1685 (tt)
  outliers start: 14
  outliers final: 9
  residues processed: 64
  average time/residue: 0.1655
  time to fit residues: 14.6153
Evaluate side-chains
  61 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   overall best weight:    1.8144

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 672 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 = 0.3879 r_free = 0.3879 target = 0.076613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.069088 restraints weight = 39507.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.070309 restraints weight = 27055.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.071054 restraints weight = 20117.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.7804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6069  Z= 0.139
  Angle     :  0.656   9.107   8279  Z= 0.333
  Chirality :  0.042   0.165    917
  Planarity :  0.005   0.047   1043
  Dihedral  :  4.465  15.753    802
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.00 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.10 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.32), residues: 725
  helix:  0.71 (0.27), residues: 381
  sheet: -0.28 (0.68), residues: 60
  loop : -0.71 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 764 
 HIS   0.005   0.001   HIS A 698 
 PHE   0.015   0.001   PHE A 614 
 TYR   0.011   0.001   TYR A 293 
 ARG   0.007   0.001   ARG A 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  312)
  hydrogen bonds       : angle       4.64513 (  903)
  covalent geometry    : bond        0.00316 ( 6069)
  covalent geometry    : angle       0.65619 ( 8279)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ARG cc_start: 0.3961 (OUTLIER) cc_final: 0.3737 (ptt180)
REVERT: A  135 MET cc_start: 0.6326 (tmm) cc_final: 0.4578 (ttm)
REVERT: A  773 PHE cc_start: 0.8231 (t80) cc_final: 0.7682 (t80)
REVERT: A  826 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6088 (m-80)
REVERT: A  864 LEU cc_start: 0.2225 (OUTLIER) cc_final: 0.1566 (tt)
  outliers start: 14
  outliers final: 9
  residues processed: 59
  average time/residue: 0.1920
  time to fit residues: 15.3708
Evaluate side-chains
  60 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  744 TYR
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 672 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 = 0.3840 r_free = 0.3840 target = 0.075019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.067075 restraints weight = 38808.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.068263 restraints weight = 26342.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.069184 restraints weight = 19979.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.8316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6069  Z= 0.179
  Angle     :  0.709   8.980   8279  Z= 0.361
  Chirality :  0.043   0.157    917
  Planarity :  0.006   0.086   1043
  Dihedral  :  4.707  18.197    802
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.24 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.78 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.31), residues: 725
  helix:  0.60 (0.27), residues: 382
  sheet: -0.19 (0.70), residues: 58
  loop : -0.88 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 779 
 HIS   0.005   0.001   HIS A 698 
 PHE   0.022   0.002   PHE A 614 
 TYR   0.012   0.002   TYR A 654 
 ARG   0.008   0.001   ARG A 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03808 (  312)
  hydrogen bonds       : angle       4.89488 (  903)
  covalent geometry    : bond        0.00395 ( 6069)
  covalent geometry    : angle       0.70855 ( 8279)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1927.97 seconds
wall clock time: 35 minutes 31.03 seconds (2131.03 seconds total)