Starting phenix.real_space_refine
on Wed May 14 06:19:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ga9_29894/05_2025/8ga9_29894.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ga9_29894/05_2025/8ga9_29894.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ga9_29894/05_2025/8ga9_29894.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ga9_29894/05_2025/8ga9_29894.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ga9_29894/05_2025/8ga9_29894.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ga9_29894/05_2025/8ga9_29894.cif"
  }
  resolution = 3.71
  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=   0.013
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: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    3840      2.51       5
     N     836      2.21       5
     O     976      1.98       5
     H    5864      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11552
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 2888
          Classifications: {'peptide': 165}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 152}
    Chain: "C"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 2888
          Classifications: {'peptide': 165}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 152}
    Chain: "E"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 2888
          Classifications: {'peptide': 165}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 152}
    Chain: "G"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 2888
          Classifications: {'peptide': 165}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 152}
  Time building chain proxies: 6.36, per 1000 atoms: 0.55
  Number of scatterers: 11552
  At special positions: 0
  Unit cell: (89.385, 88.5, 61.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     O     976      8.00
     N     836      7.00
     C    3840      6.00
     H    5864      1.00
    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: 2.86
  Conformation dependent library (CDL) restraints added in 681.9 milliseconds
  

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1296

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      92.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 10
      removed outlier: 4.236A  pdb=" N   LEU A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A   6 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 24
      removed outlier: 3.534A  pdb=" N   GLN A  16 " --> pdb=" O   PRO A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 40
      removed outlier: 3.981A  pdb=" N   GLU A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 53
      removed outlier: 3.509A  pdb=" N   LEU A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A  53 " --> pdb=" O   ARG A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 69
      removed outlier: 3.911A  pdb=" N   GLU A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 83
      removed outlier: 3.511A  pdb=" N   PHE A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   LEU A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLU A  81 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 95
      removed outlier: 3.899A  pdb=" N   ASN A  93 " --> pdb=" O   GLN A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 3.679A  pdb=" N   LYS A 124 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 139
      removed outlier: 3.718A  pdb=" N   PHE A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 153
    Processing helix  chain 'A' and resid 155 through 164
    Processing helix  chain 'C' and resid 168 through 176
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'C' and resid 192 through 206
      removed outlier: 4.122A  pdb=" N   GLU C 198 " --> pdb=" O   GLU C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 219
      removed outlier: 3.531A  pdb=" N   LEU C 212 " --> pdb=" O   GLY C 208 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU C 219 " --> pdb=" O   ARG C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 235
      removed outlier: 3.786A  pdb=" N   GLU C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 248
      removed outlier: 4.476A  pdb=" N   LEU C 241 " --> pdb=" O   GLU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 261
    Processing helix  chain 'C' and resid 264 through 277
    Processing helix  chain 'C' and resid 278 through 292
      removed outlier: 3.672A  pdb=" N   TYR C 288 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU C 289 " --> pdb=" O   PHE C 285 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS C 290 " --> pdb=" O   PHE C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 305
    Processing helix  chain 'C' and resid 307 through 319
    Processing helix  chain 'C' and resid 321 through 330
    Processing helix  chain 'E' and resid 334 through 342
    Processing helix  chain 'E' and resid 344 through 356
    Processing helix  chain 'E' and resid 358 through 372
      removed outlier: 4.255A  pdb=" N   GLU E 364 " --> pdb=" O   GLU E 360 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU E 372 " --> pdb=" O   ARG E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 374 through 385
      removed outlier: 3.602A  pdb=" N   LEU E 378 " --> pdb=" O   GLY E 374 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU E 385 " --> pdb=" O   ARG E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 387 through 401
      removed outlier: 3.535A  pdb=" N   GLN E 391 " --> pdb=" O   HIS E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 401 through 415
      removed outlier: 3.572A  pdb=" N   PHE E 405 " --> pdb=" O   ASN E 401 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS E 406 " --> pdb=" O   PRO E 402 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   LEU E 407 " --> pdb=" O   GLU E 403 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU E 412 " --> pdb=" O   PHE E 408 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 417 through 427
    Processing helix  chain 'E' and resid 430 through 443
      removed outlier: 3.748A  pdb=" N   GLN E 434 " --> pdb=" O   HIS E 430 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 444 through 458
      removed outlier: 3.683A  pdb=" N   LYS E 456 " --> pdb=" O   PHE E 452 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 460 through 472
      removed outlier: 4.611A  pdb=" N   LEU E 464 " --> pdb=" O   GLY E 460 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 473 through 485
    Processing helix  chain 'E' and resid 487 through 497
    Processing helix  chain 'G' and resid 500 through 509
    Processing helix  chain 'G' and resid 510 through 523
      removed outlier: 3.517A  pdb=" N   GLN G 514 " --> pdb=" O   PRO G 510 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 524 through 538
      removed outlier: 4.151A  pdb=" N   GLU G 530 " --> pdb=" O   GLU G 526 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU G 538 " --> pdb=" O   ARG G 534 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 540 through 551
      removed outlier: 3.849A  pdb=" N   LEU G 544 " --> pdb=" O   GLY G 540 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 553 through 566
      removed outlier: 3.610A  pdb=" N   GLU G 566 " --> pdb=" O   GLU G 562 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 570 through 581
      removed outlier: 3.736A  pdb=" N   GLU G 576 " --> pdb=" O   LYS G 572 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU G 578 " --> pdb=" O   PHE G 574 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 583 through 593
    Processing helix  chain 'G' and resid 596 through 609
    Processing helix  chain 'G' and resid 610 through 624
      removed outlier: 3.670A  pdb=" N   LYS G 622 " --> pdb=" O   PHE G 618 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 627 through 637
    Processing helix  chain 'G' and resid 639 through 651
    Processing helix  chain 'G' and resid 653 through 662

    380 hydrogen bonds defined for protein.
    1140 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: 3.65

  Time building geometry restraints manager: 3.45 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 5856
        1.13 -     1.31: 988
        1.31 -     1.48: 2108
        1.48 -     1.66: 2688
        1.66 -     1.83: 64
  Bond restraints: 11704
  Sorted by residual:
  bond pdb=" CD2 PHE G 531 "
       pdb=" HD2 PHE G 531 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" NE2 HIS G 553 "
       pdb=" HE2 HIS G 553 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   VAL E 497 "
       pdb=" H   VAL E 497 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CE1 HIS E 387 "
       pdb=" HE1 HIS E 387 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   GLN C 225 "
       pdb=" H   GLN C 225 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 11699 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 17454
        2.61 -     5.22: 3284
        5.22 -     7.83: 613
        7.83 -    10.44: 54
       10.44 -    13.05: 7
  Bond angle restraints: 21412
  Sorted by residual:
  angle pdb=" CA  ASN E 358 "
        pdb=" CB  ASN E 358 "
        pdb=" CG  ASN E 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.38   -5.78 1.00e+00 1.00e+00 3.34e+01
  angle pdb=" C   MET E 343 "
        pdb=" N   PRO E 344 "
        pdb=" CA  PRO E 344 "
      ideal   model   delta    sigma   weight residual
     119.66  123.82   -4.16 7.30e-01 1.88e+00 3.25e+01
  angle pdb=" CB  HIS C 264 "
        pdb=" CG  HIS C 264 "
        pdb=" CD2 HIS C 264 "
      ideal   model   delta    sigma   weight residual
     131.20  124.15    7.05 1.30e+00 5.92e-01 2.94e+01
  angle pdb=" CA  PHE C 200 "
        pdb=" CB  PHE C 200 "
        pdb=" CG  PHE C 200 "
      ideal   model   delta    sigma   weight residual
     113.80  108.44    5.36 1.00e+00 1.00e+00 2.88e+01
  angle pdb=" C   ASN E 401 "
        pdb=" N   PRO E 402 "
        pdb=" CA  PRO E 402 "
      ideal   model   delta    sigma   weight residual
     119.82  125.06   -5.24 9.80e-01 1.04e+00 2.86e+01
  ... (remaining 21407 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 5032
       17.71 -    35.41: 283
       35.41 -    53.11: 93
       53.11 -    70.82: 43
       70.82 -    88.52: 9
  Dihedral angle restraints: 5460
    sinusoidal: 2984
      harmonic: 2476
  Sorted by residual:
  dihedral pdb=" CA  PHE A  77 "
           pdb=" C   PHE A  77 "
           pdb=" N   GLU A  78 "
           pdb=" CA  GLU A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.02   29.98     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  ARG E 457 "
           pdb=" C   ARG E 457 "
           pdb=" N   CYS E 458 "
           pdb=" CA  CYS E 458 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.67   29.33     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  ASN G 567 "
           pdb=" C   ASN G 567 "
           pdb=" N   PRO G 568 "
           pdb=" CA  PRO G 568 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.35  -28.65     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 5457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 527
       0.087 -    0.175: 249
       0.175 -    0.262: 51
       0.262 -    0.349: 15
       0.349 -    0.436: 2
  Chirality restraints: 844
  Sorted by residual:
  chirality pdb=" CA  PHE A  77 "
            pdb=" N   PHE A  77 "
            pdb=" C   PHE A  77 "
            pdb=" CB  PHE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.76e+00
  chirality pdb=" CA  PRO E 431 "
            pdb=" N   PRO E 431 "
            pdb=" C   PRO E 431 "
            pdb=" CB  PRO E 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.35    0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CA  MET C 167 "
            pdb=" N   MET C 167 "
            pdb=" C   MET C 167 "
            pdb=" CB  MET C 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.24    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 841 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 155 "    0.096 2.00e-02 2.50e+03   8.84e-02 1.17e+02
        pdb=" CG  ASN A 155 "   -0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 155 "   -0.062 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 155 "   -0.076 2.00e-02 2.50e+03
        pdb="HD21 ASN A 155 "   -0.070 2.00e-02 2.50e+03
        pdb="HD22 ASN A 155 "    0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G 550 "   -0.129 2.00e-02 2.50e+03   5.87e-02 1.03e+02
        pdb=" CG  TYR G 550 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR G 550 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TYR G 550 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR G 550 "    0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR G 550 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR G 550 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR G 550 "   -0.118 2.00e-02 2.50e+03
        pdb=" HD1 TYR G 550 "    0.056 2.00e-02 2.50e+03
        pdb=" HD2 TYR G 550 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR G 550 "    0.006 2.00e-02 2.50e+03
        pdb=" HE2 TYR G 550 "    0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  25 "   -0.088 2.00e-02 2.50e+03   8.19e-02 1.01e+02
        pdb=" CG  ASN A  25 "    0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  25 "    0.047 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  25 "    0.082 2.00e-02 2.50e+03
        pdb="HD21 ASN A  25 "    0.060 2.00e-02 2.50e+03
        pdb="HD22 ASN A  25 "   -0.137 2.00e-02 2.50e+03
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        1.24 -     1.91: 92
        1.91 -     2.59: 10184
        2.59 -     3.26: 35690
        3.26 -     3.93: 44115
        3.93 -     4.60: 65969
  Nonbonded interactions: 156050
  Sorted by model distance:
  nonbonded pdb="HD12 LEU C 260 "
            pdb="HD11 LEU C 263 "
     model   vdw
     1.242 2.440
  nonbonded pdb=" HE2 PHE A 116 "
            pdb="HD23 LEU A 161 "
     model   vdw
     1.568 2.270
  nonbonded pdb="HD22 LEU A 106 "
            pdb="HD21 LEU A 148 "
     model   vdw
     1.614 2.440
  nonbonded pdb=" O   GLN A 102 "
            pdb="HD13 LEU A 106 "
     model   vdw
     1.636 2.620
  nonbonded pdb=" OE2 GLU A  78 "
            pdb=" HH  TYR A 122 "
     model   vdw
     1.652 2.450
  ... (remaining 156045 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
}

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=0.00 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:             4.130
  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:             0.160
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.260
  Find NCS groups from input model:        0.270
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
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      :  0.014   0.051   5840  Z= 0.819
  Angle     :  1.814   8.192   7864  Z= 1.212
  Chirality :  0.103   0.436    844
  Planarity :  0.015   0.100    996
  Dihedral  : 13.583  88.525   2304
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.31 %
  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: -2.78 (0.27), residues: 652
  helix: -1.92 (0.16), residues: 584
  sheet:  None (None), residues: 0
  loop :  1.59 (0.83), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.005   HIS G 596 
 PHE   0.100   0.015   PHE E 452 
 TYR   0.115   0.023   TYR G 550 
 ARG   0.015   0.003   ARG G 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20216 (  380)
  hydrogen bonds       : angle       7.82187 ( 1140)
  covalent geometry    : bond        0.01449 ( 5840)
  covalent geometry    : angle       1.81358 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6636 (ttpt)
REVERT: C  282 PHE cc_start: 0.8393 (t80) cc_final: 0.8058 (t80)
REVERT: C  312 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7999 (mppt)
REVERT: E  432 MET cc_start: 0.7676 (mpp) cc_final: 0.7461 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.3893
  time to fit residues: 94.1301
Evaluate side-chains
  142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   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  25 ASN
G 524 ASN
G 587 GLN
G 600 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.182340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.160848 restraints weight = 23489.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.167552 restraints weight = 11000.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.171823 restraints weight = 6303.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   5840  Z= 0.223
  Angle     :  0.787   8.513   7864  Z= 0.404
  Chirality :  0.041   0.162    844
  Planarity :  0.005   0.041    996
  Dihedral  :  5.893  28.827    708
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.02 %
    Favored  : 89.24 %
  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: -0.95 (0.29), residues: 652
  helix: -0.65 (0.18), residues: 598
  sheet:  None (None), residues: 0
  loop :  2.23 (0.97), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS E 387 
 PHE   0.022   0.002   PHE E 452 
 TYR   0.014   0.002   TYR C 227 
 ARG   0.005   0.001   ARG G 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07165 (  380)
  hydrogen bonds       : angle       5.36912 ( 1140)
  covalent geometry    : bond        0.00491 ( 5840)
  covalent geometry    : angle       0.78745 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  657 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7618 (tppt)
  outliers start: 11
  outliers final: 8
  residues processed: 149
  average time/residue: 0.3237
  time to fit residues: 67.2471
Evaluate side-chains
  133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain C residue  302 ILE
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  558 ILE
Chi-restraints excluded: chain G residue  620 TYR
Chi-restraints excluded: chain G residue  630 LEU
Chi-restraints excluded: chain G residue  641 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0670
   chunk 7 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
C 268 GLN
C 278 ASN
E 444 ASN
G 587 GLN
G 610 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.175168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.152732 restraints weight = 23442.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.159830 restraints weight = 11006.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.164362 restraints weight = 6202.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5840  Z= 0.158
  Angle     :  0.656   7.752   7864  Z= 0.331
  Chirality :  0.037   0.148    844
  Planarity :  0.005   0.036    996
  Dihedral  :  5.293  26.266    708
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  9.97 %
    Favored  : 88.13 %
  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:  0.07 (0.30), residues: 652
  helix:  0.07 (0.19), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.61 (0.95), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 596 
 PHE   0.016   0.002   PHE E 452 
 TYR   0.012   0.002   TYR C 172 
 ARG   0.002   0.000   ARG E 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05384 (  380)
  hydrogen bonds       : angle       4.78518 ( 1140)
  covalent geometry    : bond        0.00349 ( 5840)
  covalent geometry    : angle       0.65567 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ASN cc_start: 0.7003 (m-40) cc_final: 0.6761 (m-40)
REVERT: C  211 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7551 (mm-30)
REVERT: C  270 GLU cc_start: 0.6973 (tp30) cc_final: 0.6654 (tp30)
REVERT: E  424 LEU cc_start: 0.8473 (mm) cc_final: 0.8236 (mm)
REVERT: G  586 GLU cc_start: 0.6063 (mp0) cc_final: 0.5808 (mp0)
REVERT: G  657 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7713 (tppt)
  outliers start: 12
  outliers final: 6
  residues processed: 138
  average time/residue: 0.3013
  time to fit residues: 58.0391
Evaluate side-chains
  128 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  620 TYR
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
C 255 GLN
E 425 ASN
G 587 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.173284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.151224 restraints weight = 23722.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.158149 restraints weight = 11266.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.162590 restraints weight = 6401.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5840  Z= 0.180
  Angle     :  0.625   7.961   7864  Z= 0.315
  Chirality :  0.037   0.155    844
  Planarity :  0.005   0.046    996
  Dihedral  :  5.061  25.291    708
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.23 %
    Favored  : 87.03 %
  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:  0.47 (0.31), residues: 652
  helix:  0.39 (0.20), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.02 (0.99), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 387 
 PHE   0.012   0.001   PHE A 120 
 TYR   0.009   0.001   TYR A  61 
 ARG   0.002   0.000   ARG C 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04979 (  380)
  hydrogen bonds       : angle       4.67068 ( 1140)
  covalent geometry    : bond        0.00409 ( 5840)
  covalent geometry    : angle       0.62530 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ASN cc_start: 0.7146 (m-40) cc_final: 0.6850 (m-40)
REVERT: C  211 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7580 (mm-30)
REVERT: E  424 LEU cc_start: 0.8459 (mm) cc_final: 0.8215 (mm)
  outliers start: 11
  outliers final: 7
  residues processed: 128
  average time/residue: 0.3073
  time to fit residues: 54.2996
Evaluate side-chains
  125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  620 TYR
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.171753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.149339 restraints weight = 23535.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.156147 restraints weight = 11456.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.160574 restraints weight = 6638.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5840  Z= 0.182
  Angle     :  0.614   7.887   7864  Z= 0.309
  Chirality :  0.037   0.162    844
  Planarity :  0.005   0.033    996
  Dihedral  :  4.923  24.669    708
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.82 %
    Favored  : 85.13 %
  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:  0.67 (0.31), residues: 652
  helix:  0.55 (0.20), residues: 598
  sheet:  None (None), residues: 0
  loop :  0.60 (1.00), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 387 
 PHE   0.013   0.002   PHE A 120 
 TYR   0.016   0.002   TYR E 384 
 ARG   0.002   0.000   ARG C 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  380)
  hydrogen bonds       : angle       4.61557 ( 1140)
  covalent geometry    : bond        0.00415 ( 5840)
  covalent geometry    : angle       0.61360 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  211 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7607 (mm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 131
  average time/residue: 0.2798
  time to fit residues: 51.5782
Evaluate side-chains
  128 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  443 GLU
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  620 TYR
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 20 optimal weight:    0.0670
   chunk 25 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
E 477 GLN
G 587 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.172776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.150259 restraints weight = 23924.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.157175 restraints weight = 11544.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.161478 restraints weight = 6631.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5840  Z= 0.143
  Angle     :  0.583   6.947   7864  Z= 0.289
  Chirality :  0.036   0.137    844
  Planarity :  0.004   0.033    996
  Dihedral  :  4.705  24.140    708
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.72 %
    Favored  : 83.39 %
  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:  1.00 (0.32), residues: 652
  helix:  0.77 (0.20), residues: 601
  sheet:  None (None), residues: 0
  loop :  0.67 (1.03), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 387 
 PHE   0.012   0.001   PHE G 571 
 TYR   0.008   0.001   TYR C 218 
 ARG   0.001   0.000   ARG G 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04398 (  380)
  hydrogen bonds       : angle       4.33703 ( 1140)
  covalent geometry    : bond        0.00327 ( 5840)
  covalent geometry    : angle       0.58266 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  211 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7496 (mm-30)
REVERT: G  586 GLU cc_start: 0.6116 (mp0) cc_final: 0.5465 (mt-10)
  outliers start: 12
  outliers final: 7
  residues processed: 134
  average time/residue: 0.3097
  time to fit residues: 58.3693
Evaluate side-chains
  129 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  392 ILE
Chi-restraints excluded: chain E residue  443 GLU
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  620 TYR
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 57 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0870
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
E 477 GLN
G 587 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.171034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.148605 restraints weight = 23815.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.155433 restraints weight = 11429.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.159839 restraints weight = 6563.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5840  Z= 0.155
  Angle     :  0.588   7.033   7864  Z= 0.290
  Chirality :  0.036   0.147    844
  Planarity :  0.004   0.034    996
  Dihedral  :  4.651  23.972    708
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.82 %
    Favored  : 82.44 %
  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:  0.98 (0.32), residues: 652
  helix:  0.81 (0.20), residues: 607
  sheet:  None (None), residues: 0
  loop : -0.27 (1.08), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 387 
 PHE   0.011   0.001   PHE A 120 
 TYR   0.014   0.001   TYR A 147 
 ARG   0.002   0.000   ARG G 534 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04307 (  380)
  hydrogen bonds       : angle       4.35335 ( 1140)
  covalent geometry    : bond        0.00356 ( 5840)
  covalent geometry    : angle       0.58768 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  211 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7484 (mm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 126
  average time/residue: 0.2970
  time to fit residues: 52.7869
Evaluate side-chains
  129 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 123
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  392 ILE
Chi-restraints excluded: chain E residue  443 GLU
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0050
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
E 477 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.172768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.150906 restraints weight = 23512.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.157803 restraints weight = 11067.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.162227 restraints weight = 6211.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.5113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5840  Z= 0.123
  Angle     :  0.562   5.981   7864  Z= 0.275
  Chirality :  0.035   0.128    844
  Planarity :  0.004   0.040    996
  Dihedral  :  4.456  23.308    708
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 16.14 %
    Favored  : 82.59 %
  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:  1.36 (0.32), residues: 652
  helix:  1.05 (0.20), residues: 607
  sheet:  None (None), residues: 0
  loop : -0.05 (1.10), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G 596 
 PHE   0.012   0.001   PHE E 366 
 TYR   0.012   0.001   TYR A 147 
 ARG   0.001   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  380)
  hydrogen bonds       : angle       4.08162 ( 1140)
  covalent geometry    : bond        0.00282 ( 5840)
  covalent geometry    : angle       0.56231 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  211 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7435 (mm-30)
REVERT: G  587 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6279 (tm130)
REVERT: G  591 ASN cc_start: 0.6261 (m-40) cc_final: 0.5950 (m-40)
  outliers start: 8
  outliers final: 6
  residues processed: 133
  average time/residue: 0.3133
  time to fit residues: 58.4132
Evaluate side-chains
  132 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  392 ILE
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  587 GLN
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0980
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:    0.2980
   chunk 30 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
E 477 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.173989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.151542 restraints weight = 23765.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.158552 restraints weight = 11462.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.163047 restraints weight = 6537.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.5303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5840  Z= 0.124
  Angle     :  0.558   5.851   7864  Z= 0.272
  Chirality :  0.035   0.129    844
  Planarity :  0.004   0.040    996
  Dihedral  :  4.352  22.808    708
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.35 %
    Favored  : 82.91 %
  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:  1.53 (0.32), residues: 652
  helix:  1.17 (0.20), residues: 607
  sheet:  None (None), residues: 0
  loop : -0.09 (1.12), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G 596 
 PHE   0.010   0.001   PHE E 366 
 TYR   0.010   0.001   TYR A 147 
 ARG   0.002   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03876 (  380)
  hydrogen bonds       : angle       4.01669 ( 1140)
  covalent geometry    : bond        0.00293 ( 5840)
  covalent geometry    : angle       0.55822 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  587 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6106 (tm130)
REVERT: G  591 ASN cc_start: 0.6326 (m-40) cc_final: 0.6094 (m-40)
  outliers start: 11
  outliers final: 7
  residues processed: 133
  average time/residue: 0.2973
  time to fit residues: 54.8669
Evaluate side-chains
  138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  392 ILE
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  587 GLN
Chi-restraints excluded: chain G residue  620 TYR
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0050
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
G 643 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.172548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.150126 restraints weight = 23749.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.157053 restraints weight = 11433.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.161498 restraints weight = 6543.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.5428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5840  Z= 0.141
  Angle     :  0.572   6.339   7864  Z= 0.281
  Chirality :  0.036   0.137    844
  Planarity :  0.004   0.040    996
  Dihedral  :  4.334  22.724    708
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 16.14 %
    Favored  : 82.59 %
  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:  1.57 (0.32), residues: 652
  helix:  1.21 (0.20), residues: 607
  sheet:  None (None), residues: 0
  loop : -0.29 (1.11), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 596 
 PHE   0.011   0.001   PHE A  34 
 TYR   0.010   0.001   TYR A 147 
 ARG   0.001   0.000   ARG G 534 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03974 (  380)
  hydrogen bonds       : angle       4.10255 ( 1140)
  covalent geometry    : bond        0.00325 ( 5840)
  covalent geometry    : angle       0.57250 ( 7864)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  491 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8153 (ttmm)
REVERT: G  587 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6145 (tm130)
REVERT: G  591 ASN cc_start: 0.6345 (m-40) cc_final: 0.6027 (m-40)
  outliers start: 8
  outliers final: 5
  residues processed: 136
  average time/residue: 0.2906
  time to fit residues: 55.7183
Evaluate side-chains
  135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 129
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain E residue  480 LEU
Chi-restraints excluded: chain G residue  587 GLN
Chi-restraints excluded: chain G residue  646 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.169593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.147573 restraints weight = 23888.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.154346 restraints weight = 11496.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.158655 restraints weight = 6576.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.5510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5840  Z= 0.174
  Angle     :  0.592   7.360   7864  Z= 0.295
  Chirality :  0.037   0.164    844
  Planarity :  0.004   0.039    996
  Dihedral  :  4.429  23.541    708
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 16.14 %
    Favored  : 82.28 %
  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:  1.41 (0.32), residues: 652
  helix:  1.12 (0.20), residues: 607
  sheet:  None (None), residues: 0
  loop : -0.57 (1.08), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 596 
 PHE   0.013   0.001   PHE A 120 
 TYR   0.011   0.001   TYR A 147 
 ARG   0.002   0.001   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  380)
  hydrogen bonds       : angle       4.31236 ( 1140)
  covalent geometry    : bond        0.00401 ( 5840)
  covalent geometry    : angle       0.59217 ( 7864)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4003.56 seconds
wall clock time: 69 minutes 38.12 seconds (4178.12 seconds total)