Starting phenix.real_space_refine
on Fri Jul 25 03:24:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nfl_49369/07_2025/9nfl_49369_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nfl_49369/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nfl_49369/07_2025/9nfl_49369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nfl_49369/07_2025/9nfl_49369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nfl_49369/07_2025/9nfl_49369_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nfl_49369/07_2025/9nfl_49369_neut.cif"
  }
  resolution = 4.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.66, per 1000 atoms: 0.67
  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: 2.02
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.74
  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: 2.53

  Time building geometry restraints manager: 2.38 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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.830
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:4.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.720
-------------------------------------------------------------------------------
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 : 22.10
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.28), 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
 TRP   0.008   0.001   TRP A 224 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.041   0.002   PHE A 810 
 TYR   0.022   0.002   TYR A 192 
 ARG   0.003   0.000   ARG A 284 

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

*********************** 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  : 1.017 
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: 0.8802 (pt)
REVERT: A   62 LEU cc_start: 0.8972 (tp) cc_final: 0.8751 (tp)
REVERT: A   69 MET cc_start: 0.8988 (mmm) cc_final: 0.8669 (mmp)
REVERT: A   80 MET cc_start: 0.6562 (tpt) cc_final: 0.6245 (tpt)
REVERT: A  130 TYR cc_start: 0.6684 (m-80) cc_final: 0.6429 (m-80)
REVERT: A  306 SER cc_start: 0.9013 (m) cc_final: 0.8616 (p)
REVERT: A  326 PHE cc_start: 0.8499 (m-10) cc_final: 0.8224 (m-80)
REVERT: A  371 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7375 (mtm180)
REVERT: A  501 LYS cc_start: 0.8247 (tptt) cc_final: 0.7799 (tptt)
REVERT: A  543 MET cc_start: 0.8138 (mmm) cc_final: 0.7311 (mmm)
REVERT: A  719 MET cc_start: 0.8510 (mmm) cc_final: 0.8159 (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: 0.8021 (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: 0.7217 (mmm)
REVERT: A  967 TYR cc_start: 0.7714 (m-80) cc_final: 0.6878 (m-80)
REVERT: A  970 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7891 (t80)
REVERT: A  989 GLU cc_start: 0.6563 (mm-30) cc_final: 0.5391 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 203
  average time/residue: 0.2275
  time to fit residues: 62.8377
Evaluate side-chains
  173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 23 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   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 165 HIS
A 169 GLN
A 207 GLN
A 363 ASN
A 375 HIS
A 599 HIS
** A 892 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.134114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.113465 restraints weight = 21236.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.116362 restraints weight = 13516.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.118499 restraints weight = 9683.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7070  Z= 0.169
  Angle     :  0.653   8.854   9546  Z= 0.353
  Chirality :  0.044   0.192   1092
  Planarity :  0.005   0.046   1206
  Dihedral  :  4.534  24.566    954
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.07 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.28), residues: 885
  helix:  1.00 (0.20), residues: 641
  sheet: -1.00 (0.92), residues: 30
  loop : -1.70 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 148 
 HIS   0.006   0.001   HIS A 375 
 PHE   0.035   0.003   PHE A 784 
 TYR   0.026   0.002   TYR A 378 
 ARG   0.006   0.001   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04853 (  522)
  hydrogen bonds       : angle       4.67666 ( 1530)
  covalent geometry    : bond        0.00370 ( 7070)
  covalent geometry    : angle       0.65342 ( 9546)

*********************** 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
  199 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8942 (mm) cc_final: 0.8732 (pt)
REVERT: A   62 LEU cc_start: 0.9048 (tp) cc_final: 0.8774 (tp)
REVERT: A  168 MET cc_start: 0.6609 (mmt) cc_final: 0.6392 (mmt)
REVERT: A  189 ASP cc_start: 0.7797 (m-30) cc_final: 0.7162 (m-30)
REVERT: A  192 TYR cc_start: 0.9103 (t80) cc_final: 0.8834 (t80)
REVERT: A  306 SER cc_start: 0.9174 (m) cc_final: 0.8862 (p)
REVERT: A  318 ILE cc_start: 0.9771 (pt) cc_final: 0.9448 (tt)
REVERT: A  326 PHE cc_start: 0.8364 (m-10) cc_final: 0.7977 (m-80)
REVERT: A  365 GLN cc_start: 0.8873 (pt0) cc_final: 0.8321 (pp30)
REVERT: A  371 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7887 (mtp180)
REVERT: A  378 TYR cc_start: 0.8347 (m-80) cc_final: 0.8043 (m-80)
REVERT: A  409 ILE cc_start: 0.7821 (mm) cc_final: 0.7484 (mm)
REVERT: A  501 LYS cc_start: 0.8370 (tptt) cc_final: 0.8046 (tptt)
REVERT: A  511 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7526 (mm-30)
REVERT: A  543 MET cc_start: 0.8097 (mmm) cc_final: 0.7742 (mmm)
REVERT: A  745 LEU cc_start: 0.8874 (mt) cc_final: 0.8567 (tp)
REVERT: A  768 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8356 (mmtt)
REVERT: A  906 GLU cc_start: 0.7104 (tp30) cc_final: 0.5845 (tt0)
REVERT: A  967 TYR cc_start: 0.7858 (m-80) cc_final: 0.7337 (m-80)
REVERT: A  989 GLU cc_start: 0.6351 (mm-30) cc_final: 0.4963 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2944
  time to fit residues: 81.4956
Evaluate side-chains
  156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0010
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3992

-------------------------------------------------------------------------------
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 892 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.131944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.111567 restraints weight = 21115.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.114433 restraints weight = 13342.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.116457 restraints weight = 9492.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7070  Z= 0.178
  Angle     :  0.621   8.941   9546  Z= 0.335
  Chirality :  0.041   0.159   1092
  Planarity :  0.005   0.047   1206
  Dihedral  :  4.568  24.658    954
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.95 %
    Favored  : 95.93 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.29), residues: 885
  helix:  0.93 (0.20), residues: 647
  sheet: -1.10 (0.90), residues: 30
  loop : -1.72 (0.47), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 224 
 HIS   0.004   0.001   HIS A 375 
 PHE   0.062   0.002   PHE A 784 
 TYR   0.017   0.002   TYR A 870 
 ARG   0.003   0.001   ARG A 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04524 (  522)
  hydrogen bonds       : angle       4.56810 ( 1530)
  covalent geometry    : bond        0.00385 ( 7070)
  covalent geometry    : angle       0.62074 ( 9546)

*********************** 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
  184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8976 (mm) cc_final: 0.8773 (pt)
REVERT: A  175 PHE cc_start: 0.7215 (m-80) cc_final: 0.7002 (m-80)
REVERT: A  189 ASP cc_start: 0.7823 (m-30) cc_final: 0.7195 (m-30)
REVERT: A  191 VAL cc_start: 0.9138 (t) cc_final: 0.8753 (p)
REVERT: A  255 GLU cc_start: 0.6613 (tp30) cc_final: 0.5854 (mm-30)
REVERT: A  267 GLU cc_start: 0.8267 (tp30) cc_final: 0.7823 (tp30)
REVERT: A  306 SER cc_start: 0.9239 (m) cc_final: 0.8918 (p)
REVERT: A  409 ILE cc_start: 0.7888 (mm) cc_final: 0.7582 (mm)
REVERT: A  501 LYS cc_start: 0.8393 (tptt) cc_final: 0.8029 (tptt)
REVERT: A  511 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7331 (mm-30)
REVERT: A  543 MET cc_start: 0.8027 (mmm) cc_final: 0.7730 (mmp)
REVERT: A  719 MET cc_start: 0.8230 (mmm) cc_final: 0.7167 (mmp)
REVERT: A  741 MET cc_start: 0.8541 (mmp) cc_final: 0.8321 (mmm)
REVERT: A  775 MET cc_start: 0.7705 (mmm) cc_final: 0.7417 (mmp)
REVERT: A  906 GLU cc_start: 0.7077 (tp30) cc_final: 0.5926 (tt0)
REVERT: A  951 LYS cc_start: 0.9220 (pttp) cc_final: 0.8733 (ptmt)
REVERT: A  980 LEU cc_start: 0.8181 (pp) cc_final: 0.7796 (pp)
REVERT: A  989 GLU cc_start: 0.6302 (mm-30) cc_final: 0.4948 (tp30)
REVERT: A 1019 LYS cc_start: 0.7244 (tptm) cc_final: 0.6872 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1921
  time to fit residues: 48.4197
Evaluate side-chains
  148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 62 optimal weight:    0.1980
   chunk 3 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 892 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.132820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.113211 restraints weight = 20916.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.116235 restraints weight = 12968.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.118357 restraints weight = 9019.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7070  Z= 0.148
  Angle     :  0.602   8.371   9546  Z= 0.324
  Chirality :  0.041   0.203   1092
  Planarity :  0.004   0.050   1206
  Dihedral  :  4.520  26.363    954
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.39 %
    Favored  : 96.50 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.29), residues: 885
  helix:  0.97 (0.20), residues: 647
  sheet: -1.06 (0.92), residues: 30
  loop : -1.72 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.050   0.002   PHE A 784 
 TYR   0.014   0.002   TYR A 870 
 ARG   0.003   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04316 (  522)
  hydrogen bonds       : angle       4.45637 ( 1530)
  covalent geometry    : bond        0.00318 ( 7070)
  covalent geometry    : angle       0.60234 ( 9546)

*********************** 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
  184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8844 (mm) cc_final: 0.8600 (pt)
REVERT: A   62 LEU cc_start: 0.8966 (tp) cc_final: 0.8724 (tp)
REVERT: A  189 ASP cc_start: 0.7903 (m-30) cc_final: 0.7257 (m-30)
REVERT: A  191 VAL cc_start: 0.9059 (t) cc_final: 0.8649 (p)
REVERT: A  255 GLU cc_start: 0.6483 (tp30) cc_final: 0.6174 (mm-30)
REVERT: A  267 GLU cc_start: 0.8278 (tp30) cc_final: 0.7889 (tp30)
REVERT: A  306 SER cc_start: 0.9265 (m) cc_final: 0.8951 (p)
REVERT: A  326 PHE cc_start: 0.7966 (m-10) cc_final: 0.7742 (m-80)
REVERT: A  347 PHE cc_start: 0.8601 (t80) cc_final: 0.7981 (t80)
REVERT: A  378 TYR cc_start: 0.7945 (m-80) cc_final: 0.7026 (m-80)
REVERT: A  409 ILE cc_start: 0.7860 (mm) cc_final: 0.7584 (mm)
REVERT: A  501 LYS cc_start: 0.8327 (tptt) cc_final: 0.7981 (tptt)
REVERT: A  511 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7274 (mm-30)
REVERT: A  719 MET cc_start: 0.8206 (mmm) cc_final: 0.7137 (mmp)
REVERT: A  906 GLU cc_start: 0.6946 (tp30) cc_final: 0.5892 (tt0)
REVERT: A  951 LYS cc_start: 0.9088 (pttp) cc_final: 0.8663 (ptmt)
REVERT: A  967 TYR cc_start: 0.7829 (m-80) cc_final: 0.7298 (m-80)
REVERT: A  987 ASP cc_start: 0.5648 (p0) cc_final: 0.5351 (p0)
REVERT: A  989 GLU cc_start: 0.6489 (mm-30) cc_final: 0.4980 (tp30)
REVERT: A 1019 LYS cc_start: 0.7208 (tptm) cc_final: 0.6822 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1657
  time to fit residues: 41.9900
Evaluate side-chains
  156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0270
   chunk 41 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0070
   chunk 23 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0000
   chunk 45 optimal weight:    9.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.3060

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

Flipped N/Q/H residues before XYZ refinement:
A 412 ASN
** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 GLN
** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 892 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.135361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.115035 restraints weight = 20737.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.117945 restraints weight = 13191.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.120016 restraints weight = 9379.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7070  Z= 0.133
  Angle     :  0.592   8.991   9546  Z= 0.315
  Chirality :  0.040   0.147   1092
  Planarity :  0.004   0.050   1206
  Dihedral  :  4.396  23.113    954
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.50 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.29), residues: 885
  helix:  0.98 (0.20), residues: 651
  sheet: -0.80 (0.94), residues: 30
  loop : -1.75 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.051   0.002   PHE A 784 
 TYR   0.010   0.001   TYR A 870 
 ARG   0.004   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  522)
  hydrogen bonds       : angle       4.33109 ( 1530)
  covalent geometry    : bond        0.00277 ( 7070)
  covalent geometry    : angle       0.59217 ( 9546)

*********************** 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
  188 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8781 (mm) cc_final: 0.8441 (pt)
REVERT: A   69 MET cc_start: 0.8561 (mmp) cc_final: 0.8318 (mmm)
REVERT: A  189 ASP cc_start: 0.7841 (m-30) cc_final: 0.7219 (m-30)
REVERT: A  192 TYR cc_start: 0.9037 (t80) cc_final: 0.8812 (t80)
REVERT: A  255 GLU cc_start: 0.6442 (tp30) cc_final: 0.5933 (mm-30)
REVERT: A  303 LYS cc_start: 0.8529 (pttp) cc_final: 0.8312 (pttp)
REVERT: A  306 SER cc_start: 0.9284 (m) cc_final: 0.8992 (p)
REVERT: A  311 MET cc_start: 0.8421 (tpp) cc_final: 0.8059 (tpt)
REVERT: A  317 MET cc_start: 0.8201 (mmp) cc_final: 0.7821 (tpt)
REVERT: A  326 PHE cc_start: 0.8009 (m-10) cc_final: 0.7768 (m-80)
REVERT: A  347 PHE cc_start: 0.8664 (t80) cc_final: 0.7898 (t80)
REVERT: A  348 PHE cc_start: 0.8251 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  357 MET cc_start: 0.7518 (mmt) cc_final: 0.7015 (tmm)
REVERT: A  478 LEU cc_start: 0.6779 (pp) cc_final: 0.6516 (pp)
REVERT: A  511 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7260 (mm-30)
REVERT: A  719 MET cc_start: 0.8086 (mmm) cc_final: 0.7042 (mmp)
REVERT: A  741 MET cc_start: 0.8876 (mmm) cc_final: 0.8490 (mmm)
REVERT: A  882 VAL cc_start: 0.9292 (t) cc_final: 0.8846 (t)
REVERT: A  906 GLU cc_start: 0.7393 (tp30) cc_final: 0.6341 (tt0)
REVERT: A  951 LYS cc_start: 0.9064 (pttp) cc_final: 0.8767 (ptmt)
REVERT: A  967 TYR cc_start: 0.7736 (m-80) cc_final: 0.7339 (m-80)
REVERT: A  980 LEU cc_start: 0.8397 (pp) cc_final: 0.7983 (pp)
REVERT: A  989 GLU cc_start: 0.6464 (mm-30) cc_final: 0.4990 (tp30)
REVERT: A 1019 LYS cc_start: 0.7155 (tptm) cc_final: 0.6881 (tptt)
REVERT: A 1020 MET cc_start: 0.9353 (tmm) cc_final: 0.8972 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1710
  time to fit residues: 44.8244
Evaluate side-chains
  156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 81 optimal weight:    0.0870
   chunk 88 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0010
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0010
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.5772

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.134388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.114352 restraints weight = 20804.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.117239 restraints weight = 13192.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.119281 restraints weight = 9349.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7070  Z= 0.134
  Angle     :  0.604   9.601   9546  Z= 0.320
  Chirality :  0.040   0.134   1092
  Planarity :  0.004   0.048   1206
  Dihedral  :  4.412  23.490    954
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.50 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.29), residues: 885
  helix:  0.96 (0.20), residues: 652
  sheet: -0.70 (0.92), residues: 30
  loop : -1.69 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 148 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.057   0.002   PHE A 784 
 TYR   0.020   0.002   TYR A 289 
 ARG   0.003   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  522)
  hydrogen bonds       : angle       4.30903 ( 1530)
  covalent geometry    : bond        0.00288 ( 7070)
  covalent geometry    : angle       0.60382 ( 9546)

*********************** 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
  187 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8498 (mm) cc_final: 0.8081 (pt)
REVERT: A   62 LEU cc_start: 0.8951 (tp) cc_final: 0.8717 (tp)
REVERT: A   69 MET cc_start: 0.8571 (mmp) cc_final: 0.7188 (mmm)
REVERT: A  143 MET cc_start: 0.8442 (ptp) cc_final: 0.7975 (ptp)
REVERT: A  189 ASP cc_start: 0.7892 (m-30) cc_final: 0.7259 (m-30)
REVERT: A  192 TYR cc_start: 0.9036 (t80) cc_final: 0.8820 (t80)
REVERT: A  255 GLU cc_start: 0.6580 (tp30) cc_final: 0.5887 (mm-30)
REVERT: A  306 SER cc_start: 0.9305 (m) cc_final: 0.9024 (p)
REVERT: A  311 MET cc_start: 0.8817 (tpp) cc_final: 0.8286 (tpt)
REVERT: A  315 PHE cc_start: 0.8410 (m-80) cc_final: 0.8126 (m-80)
REVERT: A  317 MET cc_start: 0.8223 (mmp) cc_final: 0.7793 (tpt)
REVERT: A  318 ILE cc_start: 0.9793 (pt) cc_final: 0.8976 (pt)
REVERT: A  322 TYR cc_start: 0.8531 (m-10) cc_final: 0.7753 (m-80)
REVERT: A  347 PHE cc_start: 0.8562 (t80) cc_final: 0.7608 (t80)
REVERT: A  357 MET cc_start: 0.7793 (mmt) cc_final: 0.6835 (tmm)
REVERT: A  628 MET cc_start: 0.6547 (ptp) cc_final: 0.6335 (ptm)
REVERT: A  719 MET cc_start: 0.8036 (mmm) cc_final: 0.6984 (mmp)
REVERT: A  741 MET cc_start: 0.8889 (mmm) cc_final: 0.8463 (mmm)
REVERT: A  832 THR cc_start: 0.6802 (p) cc_final: 0.6586 (p)
REVERT: A  882 VAL cc_start: 0.9301 (t) cc_final: 0.8949 (t)
REVERT: A  951 LYS cc_start: 0.9080 (pttp) cc_final: 0.8658 (ptmt)
REVERT: A  967 TYR cc_start: 0.7715 (m-80) cc_final: 0.7322 (m-80)
REVERT: A  980 LEU cc_start: 0.8631 (pp) cc_final: 0.8366 (pp)
REVERT: A  989 GLU cc_start: 0.6520 (mm-30) cc_final: 0.4991 (tp30)
REVERT: A 1019 LYS cc_start: 0.7220 (tptm) cc_final: 0.6807 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1568
  time to fit residues: 40.8560
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  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
A 207 GLN
** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.133421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.113990 restraints weight = 20296.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.116868 restraints weight = 12664.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.118942 restraints weight = 8856.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7070  Z= 0.138
  Angle     :  0.615   9.903   9546  Z= 0.326
  Chirality :  0.041   0.125   1092
  Planarity :  0.004   0.047   1206
  Dihedral  :  4.500  32.379    954
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.39 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.28), residues: 885
  helix:  0.90 (0.20), residues: 652
  sheet:  0.21 (1.22), residues: 20
  loop : -1.65 (0.44), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 174 
 HIS   0.004   0.001   HIS A 375 
 PHE   0.055   0.002   PHE A 784 
 TYR   0.020   0.001   TYR A 289 
 ARG   0.002   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  522)
  hydrogen bonds       : angle       4.34887 ( 1530)
  covalent geometry    : bond        0.00290 ( 7070)
  covalent geometry    : angle       0.61468 ( 9546)

*********************** 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
  184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8491 (mm) cc_final: 0.8051 (pt)
REVERT: A   62 LEU cc_start: 0.8988 (tp) cc_final: 0.8700 (tp)
REVERT: A   69 MET cc_start: 0.8599 (mmp) cc_final: 0.7216 (mmm)
REVERT: A  143 MET cc_start: 0.8493 (ptp) cc_final: 0.7996 (ptp)
REVERT: A  189 ASP cc_start: 0.7921 (m-30) cc_final: 0.7294 (m-30)
REVERT: A  192 TYR cc_start: 0.9056 (t80) cc_final: 0.8804 (t80)
REVERT: A  255 GLU cc_start: 0.6438 (tp30) cc_final: 0.5841 (mm-30)
REVERT: A  306 SER cc_start: 0.9291 (m) cc_final: 0.9011 (p)
REVERT: A  311 MET cc_start: 0.8686 (tpp) cc_final: 0.8392 (tpt)
REVERT: A  317 MET cc_start: 0.8130 (mmp) cc_final: 0.7705 (tpt)
REVERT: A  318 ILE cc_start: 0.9765 (pt) cc_final: 0.8918 (pt)
REVERT: A  322 TYR cc_start: 0.8594 (m-10) cc_final: 0.7994 (m-80)
REVERT: A  357 MET cc_start: 0.7800 (mmt) cc_final: 0.6840 (tmm)
REVERT: A  378 TYR cc_start: 0.7420 (m-80) cc_final: 0.6745 (m-10)
REVERT: A  419 VAL cc_start: 0.6401 (p) cc_final: 0.6115 (t)
REVERT: A  501 LYS cc_start: 0.8189 (tptt) cc_final: 0.7943 (tptt)
REVERT: A  628 MET cc_start: 0.6798 (ptp) cc_final: 0.6572 (ptm)
REVERT: A  719 MET cc_start: 0.8006 (mmm) cc_final: 0.6982 (mmp)
REVERT: A  749 ILE cc_start: 0.8687 (tt) cc_final: 0.8439 (tt)
REVERT: A  750 PHE cc_start: 0.8184 (t80) cc_final: 0.7842 (t80)
REVERT: A  832 THR cc_start: 0.6949 (p) cc_final: 0.6574 (p)
REVERT: A  882 VAL cc_start: 0.9304 (t) cc_final: 0.8974 (t)
REVERT: A  906 GLU cc_start: 0.7098 (tp30) cc_final: 0.5871 (tt0)
REVERT: A  951 LYS cc_start: 0.9068 (pttp) cc_final: 0.8676 (ptmt)
REVERT: A  967 TYR cc_start: 0.7793 (m-80) cc_final: 0.7259 (m-80)
REVERT: A  989 GLU cc_start: 0.6463 (mm-30) cc_final: 0.4920 (tp30)
REVERT: A 1019 LYS cc_start: 0.7209 (tptm) cc_final: 0.6808 (tptt)
REVERT: A 1020 MET cc_start: 0.9337 (tmm) cc_final: 0.8993 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1631
  time to fit residues: 41.3630
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  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 50 optimal weight:    0.1980
   chunk 76 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 40 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
** A 892 GLN ** 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 = 0.4093 r_free = 0.4093 target = 0.135042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.115153 restraints weight = 20915.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.118069 restraints weight = 13193.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.120151 restraints weight = 9284.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7070  Z= 0.137
  Angle     :  0.636  10.485   9546  Z= 0.337
  Chirality :  0.042   0.222   1092
  Planarity :  0.004   0.047   1206
  Dihedral  :  4.554  32.211    954
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.16 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.28), residues: 885
  helix:  0.82 (0.20), residues: 652
  sheet: -0.19 (1.07), residues: 26
  loop : -1.59 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 224 
 HIS   0.003   0.001   HIS A 375 
 PHE   0.063   0.002   PHE A 784 
 TYR   0.016   0.001   TYR A 289 
 ARG   0.004   0.000   ARG A 471 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  522)
  hydrogen bonds       : angle       4.33303 ( 1530)
  covalent geometry    : bond        0.00293 ( 7070)
  covalent geometry    : angle       0.63640 ( 9546)

*********************** 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  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8639 (mm) cc_final: 0.8188 (pt)
REVERT: A   62 LEU cc_start: 0.9014 (tp) cc_final: 0.8774 (tp)
REVERT: A   69 MET cc_start: 0.8551 (mmp) cc_final: 0.7216 (mmm)
REVERT: A  143 MET cc_start: 0.8427 (ptp) cc_final: 0.7927 (ptp)
REVERT: A  189 ASP cc_start: 0.7857 (m-30) cc_final: 0.7236 (m-30)
REVERT: A  192 TYR cc_start: 0.9006 (t80) cc_final: 0.8796 (t80)
REVERT: A  255 GLU cc_start: 0.6498 (tp30) cc_final: 0.5952 (mm-30)
REVERT: A  306 SER cc_start: 0.9325 (m) cc_final: 0.9046 (p)
REVERT: A  311 MET cc_start: 0.8635 (tpp) cc_final: 0.8330 (tpt)
REVERT: A  317 MET cc_start: 0.8104 (mmp) cc_final: 0.7704 (tpt)
REVERT: A  318 ILE cc_start: 0.9779 (pt) cc_final: 0.8886 (pt)
REVERT: A  322 TYR cc_start: 0.8503 (m-10) cc_final: 0.8007 (m-80)
REVERT: A  348 PHE cc_start: 0.8349 (m-80) cc_final: 0.7859 (m-80)
REVERT: A  357 MET cc_start: 0.7678 (mmt) cc_final: 0.6821 (tmm)
REVERT: A  378 TYR cc_start: 0.7385 (m-80) cc_final: 0.6927 (m-80)
REVERT: A  419 VAL cc_start: 0.6502 (p) cc_final: 0.6188 (t)
REVERT: A  501 LYS cc_start: 0.8145 (tptt) cc_final: 0.7865 (tptt)
REVERT: A  628 MET cc_start: 0.6627 (ptp) cc_final: 0.6405 (ptm)
REVERT: A  719 MET cc_start: 0.7941 (mmm) cc_final: 0.6916 (mmp)
REVERT: A  749 ILE cc_start: 0.8638 (tt) cc_final: 0.8390 (tt)
REVERT: A  750 PHE cc_start: 0.7890 (t80) cc_final: 0.7516 (t80)
REVERT: A  832 THR cc_start: 0.6770 (p) cc_final: 0.6530 (p)
REVERT: A  882 VAL cc_start: 0.9306 (t) cc_final: 0.8972 (t)
REVERT: A  906 GLU cc_start: 0.7114 (tp30) cc_final: 0.5942 (tt0)
REVERT: A  951 LYS cc_start: 0.9043 (pttp) cc_final: 0.8628 (ptmt)
REVERT: A  989 GLU cc_start: 0.6570 (mm-30) cc_final: 0.4958 (tp30)
REVERT: A 1019 LYS cc_start: 0.7196 (tptm) cc_final: 0.6795 (tptt)
REVERT: A 1020 MET cc_start: 0.9338 (tmm) cc_final: 0.8965 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1534
  time to fit residues: 39.3849
Evaluate side-chains
  151 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   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 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.132911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.113377 restraints weight = 20830.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.116305 restraints weight = 13079.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.118367 restraints weight = 9164.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.4367

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= 0.146
  Angle     :  0.627   9.118   9546  Z= 0.335
  Chirality :  0.042   0.204   1092
  Planarity :  0.004   0.045   1206
  Dihedral  :  4.550  32.000    954
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.39 %
    Favored  : 96.50 %
  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 : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.28), residues: 885
  helix:  0.77 (0.20), residues: 652
  sheet: -0.07 (1.08), residues: 26
  loop : -1.57 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 224 
 HIS   0.006   0.001   HIS A 899 
 PHE   0.057   0.002   PHE A 784 
 TYR   0.021   0.001   TYR A 870 
 ARG   0.004   0.000   ARG A 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04118 (  522)
  hydrogen bonds       : angle       4.39656 ( 1530)
  covalent geometry    : bond        0.00320 ( 7070)
  covalent geometry    : angle       0.62748 ( 9546)

*********************** 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
  182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8689 (mm) cc_final: 0.8200 (pt)
REVERT: A   62 LEU cc_start: 0.8976 (tp) cc_final: 0.8665 (tp)
REVERT: A   69 MET cc_start: 0.8600 (mmp) cc_final: 0.7214 (mmm)
REVERT: A   80 MET cc_start: 0.6412 (tpt) cc_final: 0.5528 (tpt)
REVERT: A  132 ILE cc_start: 0.8412 (tt) cc_final: 0.8149 (tt)
REVERT: A  143 MET cc_start: 0.8507 (ptp) cc_final: 0.7970 (ptp)
REVERT: A  189 ASP cc_start: 0.7932 (m-30) cc_final: 0.7318 (m-30)
REVERT: A  192 TYR cc_start: 0.9043 (t80) cc_final: 0.8806 (t80)
REVERT: A  255 GLU cc_start: 0.6015 (tp30) cc_final: 0.5597 (mm-30)
REVERT: A  306 SER cc_start: 0.9353 (m) cc_final: 0.9077 (p)
REVERT: A  311 MET cc_start: 0.8611 (tpp) cc_final: 0.8345 (tpt)
REVERT: A  317 MET cc_start: 0.8138 (mmp) cc_final: 0.7726 (tpt)
REVERT: A  318 ILE cc_start: 0.9770 (pt) cc_final: 0.8887 (pt)
REVERT: A  322 TYR cc_start: 0.8579 (m-10) cc_final: 0.8072 (m-80)
REVERT: A  357 MET cc_start: 0.7732 (mmt) cc_final: 0.6843 (tmm)
REVERT: A  378 TYR cc_start: 0.7552 (m-80) cc_final: 0.7290 (m-80)
REVERT: A  419 VAL cc_start: 0.6455 (p) cc_final: 0.6153 (t)
REVERT: A  501 LYS cc_start: 0.8176 (tptt) cc_final: 0.7888 (tptt)
REVERT: A  628 MET cc_start: 0.6739 (ptp) cc_final: 0.6488 (ptm)
REVERT: A  719 MET cc_start: 0.7985 (mmm) cc_final: 0.6953 (mmp)
REVERT: A  741 MET cc_start: 0.8915 (mmm) cc_final: 0.8579 (mmm)
REVERT: A  749 ILE cc_start: 0.8297 (tt) cc_final: 0.8046 (tt)
REVERT: A  750 PHE cc_start: 0.8142 (t80) cc_final: 0.7543 (t80)
REVERT: A  882 VAL cc_start: 0.9312 (t) cc_final: 0.8988 (t)
REVERT: A  906 GLU cc_start: 0.7151 (tp30) cc_final: 0.5921 (tt0)
REVERT: A  967 TYR cc_start: 0.7721 (m-80) cc_final: 0.7182 (m-80)
REVERT: A  989 GLU cc_start: 0.6816 (mm-30) cc_final: 0.5237 (tp30)
REVERT: A 1019 LYS cc_start: 0.7214 (tptm) cc_final: 0.6756 (tptt)
REVERT: A 1020 MET cc_start: 0.9348 (tmm) cc_final: 0.8974 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1651
  time to fit residues: 41.4264
Evaluate side-chains
  156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0040
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A 892 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.133474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.114003 restraints weight = 21097.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.116934 restraints weight = 13224.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.118993 restraints weight = 9271.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.4532

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= 0.135
  Angle     :  0.637  10.852   9546  Z= 0.336
  Chirality :  0.042   0.197   1092
  Planarity :  0.004   0.047   1206
  Dihedral  :  4.534  32.175    954
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.28 %
    Favored  : 96.61 %
  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 : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.28), residues: 885
  helix:  0.75 (0.20), residues: 653
  sheet:  0.05 (1.11), residues: 26
  loop : -1.55 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 224 
 HIS   0.004   0.001   HIS A 899 
 PHE   0.058   0.002   PHE A 784 
 TYR   0.017   0.001   TYR A 289 
 ARG   0.004   0.000   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  522)
  hydrogen bonds       : angle       4.38880 ( 1530)
  covalent geometry    : bond        0.00289 ( 7070)
  covalent geometry    : angle       0.63693 ( 9546)

********************** 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
  182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.8622 (mm) cc_final: 0.8057 (pt)
REVERT: A   62 LEU cc_start: 0.8954 (tp) cc_final: 0.8724 (tp)
REVERT: A   69 MET cc_start: 0.8576 (mmp) cc_final: 0.7207 (mmm)
REVERT: A   80 MET cc_start: 0.6442 (tpt) cc_final: 0.5556 (tpt)
REVERT: A  143 MET cc_start: 0.8532 (ptp) cc_final: 0.7996 (ptp)
REVERT: A  189 ASP cc_start: 0.7938 (m-30) cc_final: 0.7319 (m-30)
REVERT: A  192 TYR cc_start: 0.9071 (t80) cc_final: 0.8818 (t80)
REVERT: A  255 GLU cc_start: 0.6004 (tp30) cc_final: 0.5730 (mm-30)
REVERT: A  306 SER cc_start: 0.9359 (m) cc_final: 0.9066 (p)
REVERT: A  317 MET cc_start: 0.8114 (mmp) cc_final: 0.7896 (tpt)
REVERT: A  318 ILE cc_start: 0.9773 (pt) cc_final: 0.8909 (pt)
REVERT: A  322 TYR cc_start: 0.8544 (m-10) cc_final: 0.8090 (m-80)
REVERT: A  348 PHE cc_start: 0.8614 (m-80) cc_final: 0.8028 (m-80)
REVERT: A  357 MET cc_start: 0.7738 (mmt) cc_final: 0.6882 (tmm)
REVERT: A  419 VAL cc_start: 0.6365 (p) cc_final: 0.6080 (t)
REVERT: A  501 LYS cc_start: 0.8106 (tptt) cc_final: 0.7771 (tptt)
REVERT: A  507 VAL cc_start: 0.8088 (p) cc_final: 0.7848 (p)
REVERT: A  628 MET cc_start: 0.6748 (ptp) cc_final: 0.6459 (ptm)
REVERT: A  719 MET cc_start: 0.7936 (mmm) cc_final: 0.6875 (mmp)
REVERT: A  741 MET cc_start: 0.8878 (mmm) cc_final: 0.8544 (mmm)
REVERT: A  749 ILE cc_start: 0.8775 (tt) cc_final: 0.8498 (tt)
REVERT: A  750 PHE cc_start: 0.8100 (t80) cc_final: 0.7501 (t80)
REVERT: A  775 MET cc_start: 0.7025 (mmm) cc_final: 0.6759 (mmm)
REVERT: A  882 VAL cc_start: 0.9284 (t) cc_final: 0.8977 (t)
REVERT: A  961 PHE cc_start: 0.8213 (t80) cc_final: 0.7734 (t80)
REVERT: A  965 MET cc_start: 0.7780 (mmm) cc_final: 0.6849 (mmm)
REVERT: A  967 TYR cc_start: 0.7763 (m-80) cc_final: 0.7158 (m-80)
REVERT: A  989 GLU cc_start: 0.6802 (mm-30) cc_final: 0.5344 (tp30)
REVERT: A 1019 LYS cc_start: 0.6793 (tptm) cc_final: 0.6294 (tptt)
REVERT: A 1020 MET cc_start: 0.9340 (tmm) cc_final: 0.8971 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1613
  time to fit residues: 41.1207
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  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 75 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 155 GLN
** A 892 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 = 0.4066 r_free = 0.4066 target = 0.132665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.112598 restraints weight = 21120.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.115357 restraints weight = 13613.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.117343 restraints weight = 9731.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.4571

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= 0.146
  Angle     :  0.644   9.318   9546  Z= 0.338
  Chirality :  0.042   0.186   1092
  Planarity :  0.004   0.045   1206
  Dihedral  :  4.532  31.695    954
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.28 %
    Favored  : 96.61 %
  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 : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.28), residues: 885
  helix:  0.82 (0.20), residues: 649
  sheet: -0.02 (1.10), residues: 26
  loop : -1.52 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 224 
 HIS   0.004   0.001   HIS A 375 
 PHE   0.056   0.002   PHE A 784 
 TYR   0.015   0.001   TYR A 289 
 ARG   0.002   0.000   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  522)
  hydrogen bonds       : angle       4.37595 ( 1530)
  covalent geometry    : bond        0.00319 ( 7070)
  covalent geometry    : angle       0.64378 ( 9546)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2659.28 seconds
wall clock time: 48 minutes 46.85 seconds (2926.85 seconds total)