Starting phenix.real_space_refine
on Wed Sep 17 08:11:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nfl_49369/09_2025/9nfl_49369_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nfl_49369/09_2025/9nfl_49369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nfl_49369/09_2025/9nfl_49369_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nfl_49369/09_2025/9nfl_49369_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nfl_49369/09_2025/9nfl_49369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nfl_49369/09_2025/9nfl_49369.map"
  }
  resolution = 4.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.047
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: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    4474      2.51       5
     N    1158      2.21       5
     O    1259      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 6936
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 893, 6936
          Classifications: {'peptide': 893}
          Link IDs: {'PTRANS': 24, 'TRANS': 868}
          Chain breaks: 3
  Time building chain proxies: 1.77, per 1000 atoms: 0.26
  Number of scatterers: 6936
  At special positions: 0
  Unit cell: (71.06, 102.85, 140.25, 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      45     16.00
     O    1259      8.00
     N    1158      7.00
     C    4474      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: 0.55
  Conformation dependent library (CDL) restraints added in 384.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1652

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 4 sheets defined
      77.7% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 56 through 96
      Proline residue:  A  78  - end of helix
      removed outlier: 4.058A  pdb=" N   MET A  96 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 168
    Processing helix  chain 'A' and resid 171 through 178
      removed outlier: 3.630A  pdb=" N   PHE A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 223
      removed outlier: 4.306A  pdb=" N   VAL A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   GLY A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   MET A 204 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 240
      removed outlier: 3.624A  pdb=" N   VAL A 229 " --> pdb=" O   LYS A 225 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 242 through 273
      removed outlier: 3.712A  pdb=" N   VAL A 247 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA A 260 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   LYS A 261 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   ALA A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 336
      removed outlier: 4.534A  pdb=" N   ARG A 284 " --> pdb=" O   SER A 280 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU A 293 " --> pdb=" O   TYR A 289 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLU A 294 " --> pdb=" O   HIS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 383
      removed outlier: 3.648A  pdb=" N   MET A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 445 through 453
      removed outlier: 4.095A  pdb=" N   ILE A 449 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 474 through 480
      removed outlier: 3.863A  pdb=" N   GLU A 480 " --> pdb=" O   ARG A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 502
    Processing helix  chain 'A' and resid 508 through 519
      removed outlier: 3.620A  pdb=" N   ILE A 512 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 530 through 534
    Processing helix  chain 'A' and resid 544 through 559
      removed outlier: 3.752A  pdb=" N   ARG A 559 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 590
      removed outlier: 4.060A  pdb=" N   LEU A 590 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 606
    Processing helix  chain 'A' and resid 623 through 630
    Processing helix  chain 'A' and resid 714 through 721
      removed outlier: 3.725A  pdb=" N   VAL A 718 " --> pdb=" O   SER A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 724
      No H-bonds generated for 'chain 'A' and resid 722 through 724'
    Processing helix  chain 'A' and resid 725 through 757
      Proline residue:  A 744  - end of helix
      removed outlier: 4.064A  pdb=" N   ALA A 747 " --> pdb=" O   GLN A 743 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   PHE A 757 " --> pdb=" O   ILE A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 816
      removed outlier: 3.556A  pdb=" N   GLN A 816 " --> pdb=" O   SER A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 823
      removed outlier: 3.780A  pdb=" N   TRP A 820 " --> pdb=" O   ASP A 817 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   PHE A 821 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ASN A 823 " --> pdb=" O   TRP A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 871
      removed outlier: 3.689A  pdb=" N   ALA A 839 " --> pdb=" O   LEU A 835 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA A 840 " --> pdb=" O   ALA A 836 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY A 847 " --> pdb=" O   GLN A 843 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   MET A 850 " --> pdb=" O   THR A 846 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   TYR A 870 " --> pdb=" O   ILE A 866 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 888
      Proline residue:  A 883  - end of helix
      removed outlier: 3.634A  pdb=" N   ALA A 888 " --> pdb=" O   ILE A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 896
      removed outlier: 3.504A  pdb=" N   LEU A 895 " --> pdb=" O   VAL A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 928
      removed outlier: 4.399A  pdb=" N   GLY A 911 " --> pdb=" O   LEU A 907 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   LYS A 912 " --> pdb=" O   GLU A 908 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   ILE A 913 " --> pdb=" O   LYS A 909 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ALA A 914 " --> pdb=" O   ALA A 910 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLU A 916 " --> pdb=" O   LYS A 912 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ARG A 922 " --> pdb=" O   ILE A 918 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   THR A 923 " --> pdb=" O   GLU A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 983
      removed outlier: 4.022A  pdb=" N   VAL A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      Proline residue:  A 944  - end of helix
      removed outlier: 4.114A  pdb=" N   ILE A 966 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   TYR A 967 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 1004
    Processing helix  chain 'A' and resid 1014 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423
      removed outlier: 4.258A  pdb=" N   LEU A 422 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 411 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423
      removed outlier: 4.258A  pdb=" N   LEU A 422 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 411 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   ILE A 409 " --> pdb=" O   GLU A 460 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   GLU A 460 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 438
      removed outlier: 6.955A  pdb=" N   ALA A 436 " --> pdb=" O   ALA A 611 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   PHE A 613 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   VAL A 438 " --> pdb=" O   PHE A 613 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLU A 620 " --> pdb=" O   GLY A 612 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 482 through 484
      removed outlier: 6.689A  pdb=" N   LEU A 564 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   VAL A 597 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   LEU A 566 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)

    522 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2220
        1.34 -     1.46: 1335
        1.46 -     1.58: 3431
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 7070
  Sorted by residual:
  bond pdb=" CA  ALA A 236 "
       pdb=" C   ALA A 236 "
    ideal  model  delta    sigma   weight residual
    1.523  1.492  0.032 1.30e-02 5.92e+03 5.92e+00
  bond pdb=" C   HIS A  73 "
       pdb=" O   HIS A  73 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.013 1.15e-02 7.56e+03 1.25e+00
  bond pdb=" CA  LEU A  77 "
       pdb=" C   LEU A  77 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 1.23e-02 6.61e+03 1.03e+00
  bond pdb=" N   ILE A 286 "
       pdb=" CA  ILE A 286 "
    ideal  model  delta    sigma   weight residual
    1.461  1.449  0.012 1.17e-02 7.31e+03 1.03e+00
  bond pdb=" CA  PHE A 746 "
       pdb=" CB  PHE A 746 "
    ideal  model  delta    sigma   weight residual
    1.529  1.544 -0.015 1.58e-02 4.01e+03 9.13e-01
  ... (remaining 7065 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 9091
        1.29 -     2.59: 353
        2.59 -     3.88: 74
        3.88 -     5.18: 23
        5.18 -     6.47: 5
  Bond angle restraints: 9546
  Sorted by residual:
  angle pdb=" N   VAL A 943 "
        pdb=" CA  VAL A 943 "
        pdb=" C   VAL A 943 "
      ideal   model   delta    sigma   weight residual
     112.35  107.52    4.83 1.20e+00 6.94e-01 1.62e+01
  angle pdb=" N   ILE A 619 "
        pdb=" CA  ILE A 619 "
        pdb=" C   ILE A 619 "
      ideal   model   delta    sigma   weight residual
     112.96  109.40    3.56 1.00e+00 1.00e+00 1.26e+01
  angle pdb=" N   VAL A 276 "
        pdb=" CA  VAL A 276 "
        pdb=" C   VAL A 276 "
      ideal   model   delta    sigma   weight residual
     111.91  109.38    2.53 8.90e-01 1.26e+00 8.06e+00
  angle pdb=" CA  VAL A 943 "
        pdb=" C   VAL A 943 "
        pdb=" N   PRO A 944 "
      ideal   model   delta    sigma   weight residual
     120.83  119.15    1.68 6.10e-01 2.69e+00 7.61e+00
  angle pdb=" N   PHE A 277 "
        pdb=" CA  PHE A 277 "
        pdb=" C   PHE A 277 "
      ideal   model   delta    sigma   weight residual
     112.24  108.83    3.41 1.28e+00 6.10e-01 7.08e+00
  ... (remaining 9541 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 3584
       16.97 -    33.93: 478
       33.93 -    50.90: 118
       50.90 -    67.86: 17
       67.86 -    84.83: 17
  Dihedral angle restraints: 4214
    sinusoidal: 1645
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" CA  ASP A 200 "
           pdb=" C   ASP A 200 "
           pdb=" N   LYS A 201 "
           pdb=" CA  LYS A 201 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  SER A 240 "
           pdb=" C   SER A 240 "
           pdb=" N   ALA A 241 "
           pdb=" CA  ALA A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.56   19.44     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  GLY A 622 "
           pdb=" C   GLY A 622 "
           pdb=" N   THR A 623 "
           pdb=" CA  THR A 623 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.69  -16.31     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4211 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 749
       0.033 -    0.066: 255
       0.066 -    0.098: 66
       0.098 -    0.131: 19
       0.131 -    0.164: 3
  Chirality restraints: 1092
  Sorted by residual:
  chirality pdb=" CB  THR A 579 "
            pdb=" CA  THR A 579 "
            pdb=" OG1 THR A 579 "
            pdb=" CG2 THR A 579 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.71e-01
  chirality pdb=" CA  ILE A 465 "
            pdb=" N   ILE A 465 "
            pdb=" C   ILE A 465 "
            pdb=" CB  ILE A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  chirality pdb=" CB  THR A 360 "
            pdb=" CA  THR A 360 "
            pdb=" OG1 THR A 360 "
            pdb=" CG2 THR A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1089 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 810 "    0.016 2.00e-02 2.50e+03   1.80e-02 5.70e+00
        pdb=" CG  PHE A 810 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 810 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 810 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 810 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 810 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 810 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 198 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.85e+00
        pdb=" C   ILE A 198 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ILE A 198 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY A 199 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 186 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   ARG A 186 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ARG A 186 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 187 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 134
        2.57 -     3.15: 6942
        3.15 -     3.73: 11645
        3.73 -     4.32: 14734
        4.32 -     4.90: 23749
  Nonbonded interactions: 57204
  Sorted by model distance:
  nonbonded pdb=" O   THR A 339 "
            pdb=" OG1 THR A 342 "
     model   vdw
     1.984 3.040
  nonbonded pdb=" O   ALA A 236 "
            pdb=" OG  SER A 240 "
     model   vdw
     1.991 3.040
  nonbonded pdb=" OE2 GLU A 196 "
            pdb=" NZ  LYS A 201 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" OG1 THR A 185 "
            pdb=" OD2 ASP A 189 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" ND2 ASN A 308 "
            pdb=" O   MET A 787 "
     model   vdw
     2.095 3.120
  ... (remaining 57199 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.050
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7070  Z= 0.180
  Angle     :  0.648   6.473   9546  Z= 0.372
  Chirality :  0.037   0.164   1092
  Planarity :  0.005   0.040   1206
  Dihedral  : 16.864  84.830   2562
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 22.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.64 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.28), residues: 885
  helix:  0.68 (0.20), residues: 636
  sheet: -1.00 (0.95), residues: 30
  loop : -2.08 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 284 
 TYR   0.022   0.002   TYR A 192 
 PHE   0.041   0.002   PHE A 810 
 TRP   0.008   0.001   TRP A 224 
 HIS   0.003   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7070)
  covalent geometry    : angle       0.64791 ( 9546)
  hydrogen bonds       : bond        0.12310 (  522)
  hydrogen bonds       : angle       6.15077 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 197
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.9281 (mm) cc_final: 0.8804 (pt)
REVERT: A   62 LEU cc_start: 0.8972 (tp) cc_final: 0.8748 (tp)
REVERT: A   69 MET cc_start: 0.8988 (mmm) cc_final: 0.8672 (mmp)
REVERT: A   80 MET cc_start: 0.6562 (tpt) cc_final: 0.6230 (tpt)
REVERT: A  130 TYR cc_start: 0.6684 (m-80) cc_final: 0.6426 (m-80)
REVERT: A  306 SER cc_start: 0.9013 (m) cc_final: 0.8619 (p)
REVERT: A  326 PHE cc_start: 0.8499 (m-10) cc_final: 0.8223 (m-80)
REVERT: A  371 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7381 (mtm180)
REVERT: A  501 LYS cc_start: 0.8247 (tptt) cc_final: 0.7796 (tptt)
REVERT: A  543 MET cc_start: 0.8138 (mmm) cc_final: 0.7308 (mmm)
REVERT: A  719 MET cc_start: 0.8510 (mmm) cc_final: 0.8195 (mmm)
REVERT: A  749 ILE cc_start: 0.8730 (tt) cc_final: 0.8328 (tp)
REVERT: A  768 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8022 (mttt)
REVERT: A  775 MET cc_start: 0.7882 (mmm) cc_final: 0.7668 (mmp)
REVERT: A  965 MET cc_start: 0.7747 (mmm) cc_final: 0.7277 (mmm)
REVERT: A  967 TYR cc_start: 0.7714 (m-80) cc_final: 0.6866 (m-80)
REVERT: A  970 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7878 (t80)
REVERT: A  989 GLU cc_start: 0.6563 (mm-30) cc_final: 0.5386 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 203
  average time/residue: 0.0747
  time to fit residues: 20.7308
Evaluate side-chains
  170 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 GLN
A 363 ASN
A 375 HIS
A 892 GLN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 ASN ** 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 = 0.4055 r_free = 0.4055 target = 0.132357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.111725 restraints weight = 21418.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.114600 restraints weight = 13632.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.116673 restraints weight = 9764.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.118164 restraints weight = 7560.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.119257 restraints weight = 6200.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7070  Z= 0.189
  Angle     :  0.685   8.072   9546  Z= 0.370
  Chirality :  0.045   0.187   1092
  Planarity :  0.005   0.046   1206
  Dihedral  :  4.643  25.189    954
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.18 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.28), residues: 885
  helix:  0.87 (0.20), residues: 641
  sheet: -1.04 (0.91), residues: 30
  loop : -1.73 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  53 
 TYR   0.032   0.002   TYR A 992 
 PHE   0.035   0.003   PHE A 868 
 TRP   0.007   0.001   TRP A 174 
 HIS   0.005   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 7070)
  covalent geometry    : angle       0.68458 ( 9546)
  hydrogen bonds       : bond        0.04917 (  522)
  hydrogen bonds       : angle       4.77475 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8971 (mm) cc_final: 0.8749 (pt)
REVERT: A   62 LEU cc_start: 0.9052 (tp) cc_final: 0.8765 (tp)
REVERT: A  132 ILE cc_start: 0.8670 (tt) cc_final: 0.8450 (tt)
REVERT: A  189 ASP cc_start: 0.7740 (m-30) cc_final: 0.7102 (m-30)
REVERT: A  192 TYR cc_start: 0.9023 (t80) cc_final: 0.8787 (t80)
REVERT: A  306 SER cc_start: 0.9166 (m) cc_final: 0.8832 (p)
REVERT: A  318 ILE cc_start: 0.9770 (pt) cc_final: 0.9438 (tt)
REVERT: A  378 TYR cc_start: 0.8062 (m-80) cc_final: 0.7769 (m-80)
REVERT: A  409 ILE cc_start: 0.7760 (mm) cc_final: 0.7434 (mm)
REVERT: A  478 LEU cc_start: 0.7496 (pp) cc_final: 0.7252 (pp)
REVERT: A  489 PRO cc_start: 0.7471 (Cg_endo) cc_final: 0.7270 (Cg_exo)
REVERT: A  501 LYS cc_start: 0.8393 (tptt) cc_final: 0.8056 (tptt)
REVERT: A  511 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7496 (mm-30)
REVERT: A  543 MET cc_start: 0.8089 (mmm) cc_final: 0.7759 (mmm)
REVERT: A  794 PHE cc_start: 0.8235 (m-80) cc_final: 0.7674 (m-80)
REVERT: A  882 VAL cc_start: 0.9264 (t) cc_final: 0.8699 (t)
REVERT: A  906 GLU cc_start: 0.7016 (tp30) cc_final: 0.5829 (tt0)
REVERT: A  967 TYR cc_start: 0.7863 (m-80) cc_final: 0.7307 (m-80)
REVERT: A  986 MET cc_start: 0.6685 (mtp) cc_final: 0.6424 (mtp)
REVERT: A  989 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5149 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0754
  time to fit residues: 19.9174
Evaluate side-chains
  149 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0670
   chunk 67 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A 165 HIS
A 169 GLN
A 599 HIS
** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.133260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.113004 restraints weight = 20605.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.115865 restraints weight = 13232.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.117875 restraints weight = 9456.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.119294 restraints weight = 7310.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.120350 restraints weight = 5995.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7070  Z= 0.141
  Angle     :  0.593   8.365   9546  Z= 0.317
  Chirality :  0.041   0.149   1092
  Planarity :  0.004   0.049   1206
  Dihedral  :  4.497  24.598    954
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.84 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.29), residues: 885
  helix:  0.95 (0.20), residues: 648
  sheet: -1.12 (0.92), residues: 30
  loop : -1.61 (0.48), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 975 
 TYR   0.013   0.001   TYR A 870 
 PHE   0.041   0.002   PHE A 784 
 TRP   0.009   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7070)
  covalent geometry    : angle       0.59308 ( 9546)
  hydrogen bonds       : bond        0.04301 (  522)
  hydrogen bonds       : angle       4.43703 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8817 (mm) cc_final: 0.8602 (pt)
REVERT: A   62 LEU cc_start: 0.9014 (tp) cc_final: 0.8641 (tp)
REVERT: A   69 MET cc_start: 0.8590 (mmp) cc_final: 0.7108 (mmm)
REVERT: A  126 PHE cc_start: 0.7885 (m-10) cc_final: 0.7617 (m-80)
REVERT: A  143 MET cc_start: 0.7964 (ptm) cc_final: 0.7266 (ptm)
REVERT: A  175 PHE cc_start: 0.7702 (m-80) cc_final: 0.7388 (m-80)
REVERT: A  189 ASP cc_start: 0.7775 (m-30) cc_final: 0.7127 (m-30)
REVERT: A  191 VAL cc_start: 0.9035 (t) cc_final: 0.8617 (p)
REVERT: A  192 TYR cc_start: 0.9066 (t80) cc_final: 0.8848 (t80)
REVERT: A  255 GLU cc_start: 0.6289 (tp30) cc_final: 0.5718 (mm-30)
REVERT: A  267 GLU cc_start: 0.8164 (tp30) cc_final: 0.7744 (tp30)
REVERT: A  306 SER cc_start: 0.9121 (m) cc_final: 0.8770 (p)
REVERT: A  315 PHE cc_start: 0.7959 (m-80) cc_final: 0.7618 (m-80)
REVERT: A  347 PHE cc_start: 0.8757 (t80) cc_final: 0.7806 (t80)
REVERT: A  371 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7793 (mtp180)
REVERT: A  409 ILE cc_start: 0.7790 (mm) cc_final: 0.7526 (mm)
REVERT: A  478 LEU cc_start: 0.7428 (pp) cc_final: 0.7195 (pp)
REVERT: A  511 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7364 (mm-30)
REVERT: A  719 MET cc_start: 0.8133 (mmm) cc_final: 0.7143 (mmp)
REVERT: A  741 MET cc_start: 0.8574 (mmp) cc_final: 0.8334 (mmm)
REVERT: A  794 PHE cc_start: 0.8146 (m-80) cc_final: 0.7661 (m-80)
REVERT: A  882 VAL cc_start: 0.9193 (t) cc_final: 0.8763 (t)
REVERT: A  906 GLU cc_start: 0.6729 (tp30) cc_final: 0.5836 (tt0)
REVERT: A  980 LEU cc_start: 0.8472 (pp) cc_final: 0.8070 (pp)
REVERT: A  987 ASP cc_start: 0.5548 (p0) cc_final: 0.5339 (p0)
REVERT: A  989 GLU cc_start: 0.6235 (mm-30) cc_final: 0.4780 (tp30)
REVERT: A 1019 LYS cc_start: 0.7199 (tptm) cc_final: 0.6839 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0699
  time to fit residues: 18.4756
Evaluate side-chains
  146 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0030
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 412 ASN
A 582 GLN
A 722 ASN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.134482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.114429 restraints weight = 20628.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.117439 restraints weight = 12918.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.119620 restraints weight = 9030.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.121235 restraints weight = 6827.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.122250 restraints weight = 5479.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7070  Z= 0.136
  Angle     :  0.596   8.756   9546  Z= 0.318
  Chirality :  0.040   0.192   1092
  Planarity :  0.004   0.049   1206
  Dihedral  :  4.414  23.786    954
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.50 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.29), residues: 885
  helix:  0.96 (0.20), residues: 649
  sheet: -0.98 (0.95), residues: 30
  loop : -1.67 (0.47), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 476 
 TYR   0.012   0.001   TYR A 992 
 PHE   0.063   0.002   PHE A 784 
 TRP   0.006   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7070)
  covalent geometry    : angle       0.59564 ( 9546)
  hydrogen bonds       : bond        0.04227 (  522)
  hydrogen bonds       : angle       4.38882 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8757 (mm) cc_final: 0.8477 (pt)
REVERT: A   62 LEU cc_start: 0.9018 (tp) cc_final: 0.8800 (tp)
REVERT: A   80 MET cc_start: 0.6636 (tpt) cc_final: 0.6366 (tpt)
REVERT: A  132 ILE cc_start: 0.8475 (tt) cc_final: 0.8239 (tt)
REVERT: A  189 ASP cc_start: 0.7821 (m-30) cc_final: 0.7187 (m-30)
REVERT: A  192 TYR cc_start: 0.9054 (t80) cc_final: 0.8766 (t80)
REVERT: A  255 GLU cc_start: 0.6375 (tp30) cc_final: 0.6062 (mm-30)
REVERT: A  267 GLU cc_start: 0.8173 (tp30) cc_final: 0.7767 (tp30)
REVERT: A  282 GLN cc_start: 0.8742 (mt0) cc_final: 0.8512 (pm20)
REVERT: A  306 SER cc_start: 0.9168 (m) cc_final: 0.8863 (p)
REVERT: A  315 PHE cc_start: 0.8083 (m-80) cc_final: 0.7727 (m-80)
REVERT: A  326 PHE cc_start: 0.7982 (m-10) cc_final: 0.7718 (m-80)
REVERT: A  378 TYR cc_start: 0.7637 (m-80) cc_final: 0.6440 (m-10)
REVERT: A  478 LEU cc_start: 0.7488 (pp) cc_final: 0.7278 (pp)
REVERT: A  501 LYS cc_start: 0.8347 (tptt) cc_final: 0.8094 (tptt)
REVERT: A  511 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7244 (mm-30)
REVERT: A  719 MET cc_start: 0.8003 (mmm) cc_final: 0.7021 (mmp)
REVERT: A  741 MET cc_start: 0.8671 (mmp) cc_final: 0.8340 (mmm)
REVERT: A  794 PHE cc_start: 0.7992 (m-80) cc_final: 0.7641 (m-80)
REVERT: A  882 VAL cc_start: 0.9278 (t) cc_final: 0.8832 (t)
REVERT: A  906 GLU cc_start: 0.6855 (tp30) cc_final: 0.5888 (tt0)
REVERT: A  965 MET cc_start: 0.8063 (mmm) cc_final: 0.7143 (mmm)
REVERT: A  967 TYR cc_start: 0.7949 (m-80) cc_final: 0.7464 (m-80)
REVERT: A  980 LEU cc_start: 0.8245 (pp) cc_final: 0.7911 (pp)
REVERT: A  987 ASP cc_start: 0.5503 (p0) cc_final: 0.5271 (p0)
REVERT: A  989 GLU cc_start: 0.6410 (mm-30) cc_final: 0.4966 (tp30)
REVERT: A 1019 LYS cc_start: 0.7190 (tptm) cc_final: 0.6903 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0739
  time to fit residues: 18.7036
Evaluate side-chains
  152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 155 GLN
** A 899 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.132349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.111885 restraints weight = 21035.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.114814 restraints weight = 13343.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.116861 restraints weight = 9455.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.118316 restraints weight = 7267.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.119082 restraints weight = 5945.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7070  Z= 0.159
  Angle     :  0.603   8.050   9546  Z= 0.322
  Chirality :  0.040   0.136   1092
  Planarity :  0.005   0.048   1206
  Dihedral  :  4.446  23.120    954
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.73 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.29), residues: 885
  helix:  0.96 (0.20), residues: 649
  sheet: -0.97 (0.93), residues: 30
  loop : -1.62 (0.47), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 371 
 TYR   0.021   0.002   TYR A 870 
 PHE   0.053   0.002   PHE A 784 
 TRP   0.005   0.001   TRP A 224 
 HIS   0.004   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7070)
  covalent geometry    : angle       0.60272 ( 9546)
  hydrogen bonds       : bond        0.04149 (  522)
  hydrogen bonds       : angle       4.42975 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8753 (mm) cc_final: 0.8425 (pt)
REVERT: A   62 LEU cc_start: 0.9054 (tp) cc_final: 0.8817 (tp)
REVERT: A  189 ASP cc_start: 0.7840 (m-30) cc_final: 0.7192 (m-30)
REVERT: A  191 VAL cc_start: 0.9024 (t) cc_final: 0.8619 (p)
REVERT: A  192 TYR cc_start: 0.9043 (t80) cc_final: 0.8829 (t80)
REVERT: A  255 GLU cc_start: 0.6436 (tp30) cc_final: 0.6165 (mm-30)
REVERT: A  306 SER cc_start: 0.9296 (m) cc_final: 0.8981 (p)
REVERT: A  311 MET cc_start: 0.8571 (tpp) cc_final: 0.8300 (tpt)
REVERT: A  326 PHE cc_start: 0.8126 (m-10) cc_final: 0.7745 (m-80)
REVERT: A  357 MET cc_start: 0.7497 (mmt) cc_final: 0.7044 (tmm)
REVERT: A  378 TYR cc_start: 0.7692 (m-80) cc_final: 0.7469 (m-80)
REVERT: A  478 LEU cc_start: 0.7562 (pp) cc_final: 0.7324 (pp)
REVERT: A  501 LYS cc_start: 0.8201 (tptt) cc_final: 0.7830 (tptt)
REVERT: A  511 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7310 (mm-30)
REVERT: A  719 MET cc_start: 0.8135 (mmm) cc_final: 0.7092 (mmp)
REVERT: A  741 MET cc_start: 0.8592 (mmp) cc_final: 0.8354 (mmm)
REVERT: A  771 PHE cc_start: 0.7246 (t80) cc_final: 0.7043 (t80)
REVERT: A  794 PHE cc_start: 0.8018 (m-80) cc_final: 0.7661 (m-80)
REVERT: A  882 VAL cc_start: 0.9311 (t) cc_final: 0.8925 (t)
REVERT: A  927 LEU cc_start: 0.9200 (mt) cc_final: 0.8983 (mt)
REVERT: A  965 MET cc_start: 0.8051 (mmm) cc_final: 0.7139 (mmm)
REVERT: A  989 GLU cc_start: 0.6404 (mm-30) cc_final: 0.4960 (tp30)
REVERT: A 1019 LYS cc_start: 0.7288 (tptm) cc_final: 0.6885 (tptt)
REVERT: A 1020 MET cc_start: 0.9312 (tmm) cc_final: 0.8938 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0741
  time to fit residues: 18.3106
Evaluate side-chains
  145 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 4 optimal weight:    0.1980
   chunk 81 optimal weight:    0.9980
   chunk 37 optimal weight:    0.2980
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 155 GLN
** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 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 = 0.4072 r_free = 0.4072 target = 0.133733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.114168 restraints weight = 20513.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.117135 restraints weight = 12776.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.119238 restraints weight = 8909.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.120782 restraints weight = 6747.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.121872 restraints weight = 5413.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7070  Z= 0.137
  Angle     :  0.607   8.012   9546  Z= 0.324
  Chirality :  0.041   0.133   1092
  Planarity :  0.004   0.048   1206
  Dihedral  :  4.429  22.164    954
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.28 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.29), residues: 885
  helix:  0.86 (0.20), residues: 654
  sheet: -0.91 (0.93), residues: 30
  loop : -1.57 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 371 
 TYR   0.019   0.002   TYR A 289 
 PHE   0.049   0.002   PHE A 784 
 TRP   0.005   0.001   TRP A 148 
 HIS   0.002   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7070)
  covalent geometry    : angle       0.60675 ( 9546)
  hydrogen bonds       : bond        0.04177 (  522)
  hydrogen bonds       : angle       4.43460 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8512 (mm) cc_final: 0.8083 (pt)
REVERT: A   62 LEU cc_start: 0.8989 (tp) cc_final: 0.8777 (tp)
REVERT: A   69 MET cc_start: 0.8793 (mmm) cc_final: 0.7260 (mmm)
REVERT: A  189 ASP cc_start: 0.7889 (m-30) cc_final: 0.7246 (m-30)
REVERT: A  192 TYR cc_start: 0.9061 (t80) cc_final: 0.8758 (t80)
REVERT: A  255 GLU cc_start: 0.6269 (tp30) cc_final: 0.5766 (mm-30)
REVERT: A  282 GLN cc_start: 0.8777 (mt0) cc_final: 0.8245 (pm20)
REVERT: A  306 SER cc_start: 0.9270 (m) cc_final: 0.8966 (p)
REVERT: A  311 MET cc_start: 0.8572 (tpp) cc_final: 0.8322 (tpt)
REVERT: A  317 MET cc_start: 0.8121 (mmp) cc_final: 0.7662 (tpt)
REVERT: A  318 ILE cc_start: 0.9782 (pt) cc_final: 0.9004 (pt)
REVERT: A  322 TYR cc_start: 0.8602 (m-10) cc_final: 0.7764 (m-80)
REVERT: A  357 MET cc_start: 0.7469 (mmt) cc_final: 0.7019 (tmm)
REVERT: A  378 TYR cc_start: 0.7555 (m-80) cc_final: 0.7275 (m-80)
REVERT: A  478 LEU cc_start: 0.7516 (pp) cc_final: 0.7287 (pp)
REVERT: A  501 LYS cc_start: 0.8176 (tptt) cc_final: 0.7757 (tptt)
REVERT: A  511 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7318 (mm-30)
REVERT: A  719 MET cc_start: 0.8012 (mmm) cc_final: 0.6973 (mmp)
REVERT: A  741 MET cc_start: 0.8672 (mmp) cc_final: 0.8364 (mmm)
REVERT: A  771 PHE cc_start: 0.7322 (t80) cc_final: 0.7118 (t80)
REVERT: A  775 MET cc_start: 0.7565 (mmt) cc_final: 0.7201 (mmm)
REVERT: A  794 PHE cc_start: 0.7938 (m-80) cc_final: 0.7649 (m-80)
REVERT: A  882 VAL cc_start: 0.9283 (t) cc_final: 0.8916 (t)
REVERT: A  967 TYR cc_start: 0.7869 (m-80) cc_final: 0.7355 (m-80)
REVERT: A  989 GLU cc_start: 0.6457 (mm-30) cc_final: 0.4970 (tp30)
REVERT: A 1019 LYS cc_start: 0.7199 (tptm) cc_final: 0.6804 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0731
  time to fit residues: 19.0486
Evaluate side-chains
  155 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
** A 549 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 = 0.4061 r_free = 0.4061 target = 0.132404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.112825 restraints weight = 20641.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.115770 restraints weight = 12853.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.117847 restraints weight = 8989.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.119330 restraints weight = 6832.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.120416 restraints weight = 5505.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7070  Z= 0.144
  Angle     :  0.613   8.279   9546  Z= 0.326
  Chirality :  0.041   0.177   1092
  Planarity :  0.004   0.046   1206
  Dihedral  :  4.416  20.709    954
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.50 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.29), residues: 885
  helix:  0.79 (0.20), residues: 654
  sheet: -0.93 (0.91), residues: 30
  loop : -1.63 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 479 
 TYR   0.016   0.002   TYR A 289 
 PHE   0.049   0.002   PHE A 784 
 TRP   0.007   0.001   TRP A 224 
 HIS   0.004   0.001   HIS A 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7070)
  covalent geometry    : angle       0.61323 ( 9546)
  hydrogen bonds       : bond        0.04119 (  522)
  hydrogen bonds       : angle       4.40108 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8578 (mm) cc_final: 0.8097 (pt)
REVERT: A   62 LEU cc_start: 0.9001 (tp) cc_final: 0.8780 (tp)
REVERT: A   69 MET cc_start: 0.8504 (mmm) cc_final: 0.7046 (mmm)
REVERT: A  189 ASP cc_start: 0.7882 (m-30) cc_final: 0.7240 (m-30)
REVERT: A  192 TYR cc_start: 0.9058 (t80) cc_final: 0.8759 (t80)
REVERT: A  255 GLU cc_start: 0.6326 (tp30) cc_final: 0.5736 (mm-30)
REVERT: A  306 SER cc_start: 0.9304 (m) cc_final: 0.9002 (p)
REVERT: A  311 MET cc_start: 0.8557 (tpp) cc_final: 0.8355 (tpt)
REVERT: A  317 MET cc_start: 0.8084 (mmp) cc_final: 0.7658 (tpt)
REVERT: A  318 ILE cc_start: 0.9814 (pt) cc_final: 0.9436 (tt)
REVERT: A  347 PHE cc_start: 0.8922 (t80) cc_final: 0.8007 (t80)
REVERT: A  357 MET cc_start: 0.7428 (mmt) cc_final: 0.7019 (tmm)
REVERT: A  419 VAL cc_start: 0.6360 (p) cc_final: 0.6074 (t)
REVERT: A  501 LYS cc_start: 0.8129 (tptt) cc_final: 0.7707 (tptt)
REVERT: A  628 MET cc_start: 0.6752 (ptp) cc_final: 0.6352 (ptm)
REVERT: A  719 MET cc_start: 0.8009 (mmm) cc_final: 0.6998 (mmp)
REVERT: A  741 MET cc_start: 0.8636 (mmp) cc_final: 0.8358 (mmm)
REVERT: A  771 PHE cc_start: 0.7210 (t80) cc_final: 0.6973 (t80)
REVERT: A  794 PHE cc_start: 0.7968 (m-80) cc_final: 0.7639 (m-80)
REVERT: A  832 THR cc_start: 0.6841 (p) cc_final: 0.6593 (p)
REVERT: A  882 VAL cc_start: 0.9302 (t) cc_final: 0.8947 (t)
REVERT: A  927 LEU cc_start: 0.9181 (mt) cc_final: 0.8976 (mt)
REVERT: A  967 TYR cc_start: 0.7880 (m-80) cc_final: 0.7393 (m-80)
REVERT: A  989 GLU cc_start: 0.6758 (mm-30) cc_final: 0.5204 (tp30)
REVERT: A 1019 LYS cc_start: 0.7260 (tptm) cc_final: 0.6915 (tptt)
REVERT: A 1020 MET cc_start: 0.9315 (tmm) cc_final: 0.8962 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0713
  time to fit residues: 18.3118
Evaluate side-chains
  147 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 ASN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 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 = 0.4068 r_free = 0.4068 target = 0.133054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.113617 restraints weight = 20706.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.116562 restraints weight = 12784.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.118662 restraints weight = 8908.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.120168 restraints weight = 6712.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.121225 restraints weight = 5382.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7070  Z= 0.143
  Angle     :  0.628   7.687   9546  Z= 0.333
  Chirality :  0.042   0.223   1092
  Planarity :  0.004   0.048   1206
  Dihedral  :  4.412  19.762    954
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.16 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.28), residues: 885
  helix:  0.73 (0.20), residues: 655
  sheet: -0.20 (1.22), residues: 20
  loop : -1.66 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 476 
 TYR   0.018   0.002   TYR A 289 
 PHE   0.044   0.002   PHE A 784 
 TRP   0.006   0.001   TRP A 224 
 HIS   0.010   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7070)
  covalent geometry    : angle       0.62842 ( 9546)
  hydrogen bonds       : bond        0.04114 (  522)
  hydrogen bonds       : angle       4.43316 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8581 (mm) cc_final: 0.8098 (pt)
REVERT: A   62 LEU cc_start: 0.8994 (tp) cc_final: 0.8771 (tp)
REVERT: A   69 MET cc_start: 0.8516 (mmm) cc_final: 0.7065 (mmm)
REVERT: A  132 ILE cc_start: 0.8209 (tt) cc_final: 0.7987 (tt)
REVERT: A  189 ASP cc_start: 0.7888 (m-30) cc_final: 0.7251 (m-30)
REVERT: A  192 TYR cc_start: 0.9059 (t80) cc_final: 0.8764 (t80)
REVERT: A  255 GLU cc_start: 0.6179 (tp30) cc_final: 0.5647 (mm-30)
REVERT: A  303 LYS cc_start: 0.8492 (pttp) cc_final: 0.8290 (mtmm)
REVERT: A  306 SER cc_start: 0.9363 (m) cc_final: 0.9077 (p)
REVERT: A  311 MET cc_start: 0.8550 (tpp) cc_final: 0.8341 (tpt)
REVERT: A  317 MET cc_start: 0.8139 (mmp) cc_final: 0.7742 (tpt)
REVERT: A  318 ILE cc_start: 0.9820 (pt) cc_final: 0.8960 (pt)
REVERT: A  322 TYR cc_start: 0.8638 (m-10) cc_final: 0.8048 (m-80)
REVERT: A  357 MET cc_start: 0.7412 (mmt) cc_final: 0.7032 (tmm)
REVERT: A  378 TYR cc_start: 0.7677 (m-80) cc_final: 0.6809 (m-80)
REVERT: A  419 VAL cc_start: 0.6458 (p) cc_final: 0.6135 (t)
REVERT: A  501 LYS cc_start: 0.8100 (tptt) cc_final: 0.7620 (tptt)
REVERT: A  507 VAL cc_start: 0.8009 (p) cc_final: 0.7804 (p)
REVERT: A  628 MET cc_start: 0.6871 (ptp) cc_final: 0.6593 (ptm)
REVERT: A  719 MET cc_start: 0.7998 (mmm) cc_final: 0.6963 (mmp)
REVERT: A  741 MET cc_start: 0.8719 (mmp) cc_final: 0.8394 (mmm)
REVERT: A  750 PHE cc_start: 0.8164 (t80) cc_final: 0.7927 (t80)
REVERT: A  771 PHE cc_start: 0.7310 (t80) cc_final: 0.7061 (t80)
REVERT: A  794 PHE cc_start: 0.8015 (m-80) cc_final: 0.7646 (m-80)
REVERT: A  832 THR cc_start: 0.6803 (p) cc_final: 0.6553 (p)
REVERT: A  882 VAL cc_start: 0.9300 (t) cc_final: 0.8953 (t)
REVERT: A  906 GLU cc_start: 0.6555 (tp30) cc_final: 0.5041 (tt0)
REVERT: A  967 TYR cc_start: 0.7880 (m-80) cc_final: 0.7307 (m-80)
REVERT: A  987 ASP cc_start: 0.5529 (p0) cc_final: 0.5311 (p0)
REVERT: A  989 GLU cc_start: 0.6706 (mm-30) cc_final: 0.5118 (tp30)
REVERT: A 1020 MET cc_start: 0.9286 (tmm) cc_final: 0.8934 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0691
  time to fit residues: 18.0588
Evaluate side-chains
  152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0980
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 ASN
** A 899 HIS ** 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 = 0.4070 r_free = 0.4070 target = 0.133141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.113658 restraints weight = 20651.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.116596 restraints weight = 12809.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.118665 restraints weight = 8941.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.120139 restraints weight = 6793.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.121249 restraints weight = 5481.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.4412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7070  Z= 0.134
  Angle     :  0.627  10.999   9546  Z= 0.329
  Chirality :  0.042   0.211   1092
  Planarity :  0.004   0.045   1206
  Dihedral  :  4.404  17.981    954
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.39 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.28), residues: 885
  helix:  0.75 (0.20), residues: 654
  sheet: -0.20 (1.23), residues: 20
  loop : -1.56 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 476 
 TYR   0.018   0.001   TYR A 289 
 PHE   0.046   0.002   PHE A 784 
 TRP   0.006   0.001   TRP A 872 
 HIS   0.004   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7070)
  covalent geometry    : angle       0.62748 ( 9546)
  hydrogen bonds       : bond        0.03983 (  522)
  hydrogen bonds       : angle       4.37392 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8704 (mm) cc_final: 0.8226 (pt)
REVERT: A   62 LEU cc_start: 0.8983 (tp) cc_final: 0.8765 (tp)
REVERT: A   69 MET cc_start: 0.8341 (mmm) cc_final: 0.7155 (mmm)
REVERT: A  189 ASP cc_start: 0.7892 (m-30) cc_final: 0.7241 (m-30)
REVERT: A  192 TYR cc_start: 0.9067 (t80) cc_final: 0.8760 (t80)
REVERT: A  255 GLU cc_start: 0.5962 (tp30) cc_final: 0.5637 (mm-30)
REVERT: A  306 SER cc_start: 0.9305 (m) cc_final: 0.9001 (p)
REVERT: A  317 MET cc_start: 0.8123 (mmp) cc_final: 0.7734 (tpt)
REVERT: A  318 ILE cc_start: 0.9820 (pt) cc_final: 0.8939 (pt)
REVERT: A  322 TYR cc_start: 0.8603 (m-10) cc_final: 0.8086 (m-80)
REVERT: A  326 PHE cc_start: 0.8538 (m-80) cc_final: 0.8310 (m-80)
REVERT: A  348 PHE cc_start: 0.8352 (m-80) cc_final: 0.7780 (m-80)
REVERT: A  357 MET cc_start: 0.7627 (mmt) cc_final: 0.6832 (tmm)
REVERT: A  378 TYR cc_start: 0.7587 (m-80) cc_final: 0.7059 (m-80)
REVERT: A  419 VAL cc_start: 0.6402 (p) cc_final: 0.6103 (t)
REVERT: A  501 LYS cc_start: 0.8040 (tptt) cc_final: 0.7502 (tptt)
REVERT: A  628 MET cc_start: 0.6746 (ptp) cc_final: 0.6430 (ptm)
REVERT: A  719 MET cc_start: 0.7855 (mmm) cc_final: 0.6871 (mmp)
REVERT: A  771 PHE cc_start: 0.7622 (t80) cc_final: 0.7398 (t80)
REVERT: A  794 PHE cc_start: 0.8045 (m-80) cc_final: 0.7670 (m-80)
REVERT: A  832 THR cc_start: 0.6855 (p) cc_final: 0.6439 (p)
REVERT: A  965 MET cc_start: 0.8021 (mmm) cc_final: 0.7232 (mmm)
REVERT: A  989 GLU cc_start: 0.6856 (mm-30) cc_final: 0.5325 (tp30)
REVERT: A 1020 MET cc_start: 0.9316 (tmm) cc_final: 0.8929 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0659
  time to fit residues: 16.6994
Evaluate side-chains
  154 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0000
   chunk 42 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 947 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.134413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.114249 restraints weight = 21148.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.117191 restraints weight = 13298.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.119271 restraints weight = 9392.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.120724 restraints weight = 7202.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.121796 restraints weight = 5864.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7070  Z= 0.131
  Angle     :  0.628   8.832   9546  Z= 0.330
  Chirality :  0.041   0.196   1092
  Planarity :  0.004   0.047   1206
  Dihedral  :  4.336  17.535    954
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.16 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.28), residues: 885
  helix:  0.75 (0.20), residues: 654
  sheet: -0.23 (1.23), residues: 20
  loop : -1.58 (0.45), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 479 
 TYR   0.017   0.001   TYR A 289 
 PHE   0.044   0.002   PHE A 784 
 TRP   0.006   0.001   TRP A 224 
 HIS   0.004   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7070)
  covalent geometry    : angle       0.62791 ( 9546)
  hydrogen bonds       : bond        0.04051 (  522)
  hydrogen bonds       : angle       4.33469 ( 1530)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8667 (mm) cc_final: 0.8125 (pt)
REVERT: A   62 LEU cc_start: 0.8978 (tp) cc_final: 0.8769 (tp)
REVERT: A   69 MET cc_start: 0.8321 (mmm) cc_final: 0.8006 (mmm)
REVERT: A  189 ASP cc_start: 0.7841 (m-30) cc_final: 0.7210 (m-30)
REVERT: A  192 TYR cc_start: 0.9037 (t80) cc_final: 0.8766 (t80)
REVERT: A  255 GLU cc_start: 0.5776 (tp30) cc_final: 0.5338 (mm-30)
REVERT: A  306 SER cc_start: 0.9366 (m) cc_final: 0.9119 (p)
REVERT: A  315 PHE cc_start: 0.8136 (m-80) cc_final: 0.7934 (m-80)
REVERT: A  317 MET cc_start: 0.8104 (mmp) cc_final: 0.7736 (tpt)
REVERT: A  318 ILE cc_start: 0.9817 (pt) cc_final: 0.8959 (pt)
REVERT: A  322 TYR cc_start: 0.8567 (m-10) cc_final: 0.8054 (m-80)
REVERT: A  357 MET cc_start: 0.7541 (mmt) cc_final: 0.6845 (tmm)
REVERT: A  378 TYR cc_start: 0.7553 (m-80) cc_final: 0.7353 (m-80)
REVERT: A  419 VAL cc_start: 0.6367 (p) cc_final: 0.6071 (t)
REVERT: A  479 ARG cc_start: 0.6144 (mmt90) cc_final: 0.5903 (mmt90)
REVERT: A  501 LYS cc_start: 0.8011 (tptt) cc_final: 0.7467 (tptt)
REVERT: A  507 VAL cc_start: 0.8048 (p) cc_final: 0.7759 (p)
REVERT: A  628 MET cc_start: 0.6728 (ptp) cc_final: 0.6407 (ptm)
REVERT: A  719 MET cc_start: 0.8297 (mmm) cc_final: 0.7775 (mmp)
REVERT: A  741 MET cc_start: 0.8722 (mmp) cc_final: 0.8406 (mmm)
REVERT: A  771 PHE cc_start: 0.7525 (t80) cc_final: 0.7313 (t80)
REVERT: A  794 PHE cc_start: 0.7556 (m-80) cc_final: 0.7220 (m-80)
REVERT: A  832 THR cc_start: 0.6808 (p) cc_final: 0.6409 (p)
REVERT: A  965 MET cc_start: 0.7920 (mmm) cc_final: 0.7141 (mmm)
REVERT: A  967 TYR cc_start: 0.7702 (m-80) cc_final: 0.7188 (m-80)
REVERT: A  989 GLU cc_start: 0.6805 (mm-30) cc_final: 0.5288 (tp30)
REVERT: A 1020 MET cc_start: 0.9300 (tmm) cc_final: 0.8940 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0669
  time to fit residues: 17.1422
Evaluate side-chains
  160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0670
   chunk 8 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 ASN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 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 = 0.4088 r_free = 0.4088 target = 0.134533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.114396 restraints weight = 20956.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.117292 restraints weight = 13327.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.119345 restraints weight = 9481.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.120784 restraints weight = 7289.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.121833 restraints weight = 5970.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.4662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7070  Z= 0.128
  Angle     :  0.617   8.371   9546  Z= 0.322
  Chirality :  0.041   0.191   1092
  Planarity :  0.004   0.045   1206
  Dihedral  :  4.301  17.707    954
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.28 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.28), residues: 885
  helix:  0.78 (0.20), residues: 650
  sheet: -0.42 (1.19), residues: 20
  loop : -1.62 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 479 
 TYR   0.016   0.001   TYR A 289 
 PHE   0.047   0.002   PHE A 784 
 TRP   0.014   0.001   TRP A 979 
 HIS   0.004   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7070)
  covalent geometry    : angle       0.61693 ( 9546)
  hydrogen bonds       : bond        0.03922 (  522)
  hydrogen bonds       : angle       4.28775 ( 1530)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1311.63 seconds
wall clock time: 23 minutes 31.12 seconds (1411.12 seconds total)