Starting phenix.real_space_refine
on Tue Nov 18 03:29:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iu1_60886/11_2025/9iu1_60886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iu1_60886/11_2025/9iu1_60886.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iu1_60886/11_2025/9iu1_60886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iu1_60886/11_2025/9iu1_60886.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iu1_60886/11_2025/9iu1_60886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iu1_60886/11_2025/9iu1_60886.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic.
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      37      5.16       5
     C    4222      2.51       5
     N    1076      2.21       5
     O    1268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6603
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1557
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 12, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.12, per 1000 atoms: 0.32
  Number of scatterers: 6603
  At special positions: 0
  Unit cell: (87.435, 86.43, 116.58, 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      37     16.00
     O    1268      8.00
     N    1076      7.00
     C    4222      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 524 " distance=2.03

  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
  Links applied
    ALPHA1-3
      " BMA F   3 " - " MAN F   4 "
    ALPHA1-6
      " BMA F   3 " - " MAN F   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A 322 "
      " NAG B1300 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  53 "
      " NAG D   1 " - " ASN A 546 "
      " NAG E   1 " - " ASN A  90 "
      " NAG F   1 " - " ASN A 103 "
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 393.6 milliseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      52.4% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.697A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 92 through 103
    Processing helix  chain 'A' and resid 109 through 130
      removed outlier: 3.822A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 152
    Processing helix  chain 'A' and resid 157 through 174
      removed outlier: 4.598A  pdb=" N   GLU A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 3.791A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 221 through 249
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 276 through 283
      removed outlier: 3.814A  pdb=" N   SER A 280 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU A 281 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR A 282 " --> pdb=" O   TYR A 279 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL A 283 " --> pdb=" O   SER A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 300
      removed outlier: 3.734A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.859A  pdb=" N   PHE A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.602A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 411
      removed outlier: 4.283A  pdb=" N   HIS A 401 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLU A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 466
      removed outlier: 4.049A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LEU A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 469 through 485
      removed outlier: 4.463A  pdb=" N   MET A 474 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   LYS A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 534
      removed outlier: 4.544A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.990A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ARG A 559 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 4.266A  pdb=" N   LYS B 386 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.299A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134
      removed outlier: 3.780A  pdb=" N   VAL A 132 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 142 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   GLU A 140 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.839A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 349
    Processing sheet with id=AA4, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.640A  pdb=" N   ILE B 358 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 512 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474

    281 hydrogen bonds defined for protein.
    810 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2077
        1.34 -     1.46: 1507
        1.46 -     1.58: 3149
        1.58 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 6791
  Sorted by residual:
  bond pdb=" C1  MAN F   4 "
       pdb=" C2  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.570 -0.044 2.00e-02 2.50e+03 4.82e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.555 -0.036 2.00e-02 2.50e+03 3.20e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.55e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" C1  BMA F   3 "
       pdb=" C2  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.37e+00
  ... (remaining 6786 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 8859
        1.31 -     2.61: 285
        2.61 -     3.92: 54
        3.92 -     5.23: 22
        5.23 -     6.53: 10
  Bond angle restraints: 9230
  Sorted by residual:
  angle pdb=" C   ASN B 417 "
        pdb=" N   ILE B 418 "
        pdb=" CA  ILE B 418 "
      ideal   model   delta    sigma   weight residual
     120.60  124.24   -3.64 1.29e+00 6.01e-01 7.97e+00
  angle pdb=" N   THR B 522 "
        pdb=" CA  THR B 522 "
        pdb=" C   THR B 522 "
      ideal   model   delta    sigma   weight residual
     110.80  116.40   -5.60 2.13e+00 2.20e-01 6.90e+00
  angle pdb=" CA  ILE A 468 "
        pdb=" C   ILE A 468 "
        pdb=" N   PRO A 469 "
      ideal   model   delta    sigma   weight residual
     116.57  118.99   -2.42 9.80e-01 1.04e+00 6.12e+00
  angle pdb=" N   LEU A 450 "
        pdb=" CA  LEU A 450 "
        pdb=" C   LEU A 450 "
      ideal   model   delta    sigma   weight residual
     109.81  114.92   -5.11 2.21e+00 2.05e-01 5.34e+00
  angle pdb=" C   ASP B 420 "
        pdb=" N   TYR B 421 "
        pdb=" CA  TYR B 421 "
      ideal   model   delta    sigma   weight residual
     121.98  118.71    3.27 1.53e+00 4.27e-01 4.57e+00
  ... (remaining 9225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.08: 3782
       22.08 -    44.17: 317
       44.17 -    66.25: 47
       66.25 -    88.34: 22
       88.34 -   110.42: 10
  Dihedral angle restraints: 4178
    sinusoidal: 1857
      harmonic: 2321
  Sorted by residual:
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.61   75.61     1      1.00e+01 1.00e-02 7.21e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 524 "
           pdb=" CB  CYS B 524 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.37  -45.37     1      1.00e+01 1.00e-02 2.86e+01
  dihedral pdb=" CA  ALA B 521 "
           pdb=" C   ALA B 521 "
           pdb=" N   THR B 522 "
           pdb=" CA  THR B 522 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 4175 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 863
       0.061 -    0.121: 125
       0.121 -    0.182: 11
       0.182 -    0.242: 1
       0.242 -    0.303: 3
  Chirality restraints: 1003
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 546 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.84e+00
  ... (remaining 1000 not shown)

  Planarity restraints: 1179
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 199 "    0.014 2.00e-02 2.50e+03   1.51e-02 4.57e+00
        pdb=" CG  TYR A 199 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 199 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 199 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 199 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 199 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 199 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 199 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 477 "   -0.013 2.00e-02 2.50e+03   1.32e-02 4.35e+00
        pdb=" CG  TRP A 477 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 477 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 477 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 477 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 477 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 477 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 477 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 477 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 477 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 414 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.20e+00
        pdb=" N   PRO A 415 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 415 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 415 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1176 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1303
        2.77 -     3.30: 6581
        3.30 -     3.84: 11079
        3.84 -     4.37: 11746
        4.37 -     4.90: 19875
  Nonbonded interactions: 50584
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 393 "
            pdb=" OD1 ASN B 394 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG1 THR B 356 "
            pdb=" O   ALA B 397 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER A 411 "
            pdb=" OE1 GLN A 526 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG1 THR A 365 "
            pdb=" OD1 ASP A 367 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH2 ARG A 482 "
            pdb=" O   THR A 608 "
     model   vdw
     2.303 3.120
  ... (remaining 50579 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             5.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6811  Z= 0.159
  Angle     :  0.625  11.220   9284  Z= 0.299
  Chirality :  0.045   0.303   1003
  Planarity :  0.003   0.037   1173
  Dihedral  : 17.138 110.421   2670
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.31), residues: 786
  helix:  1.93 (0.29), residues: 361
  sheet:  2.25 (1.21), residues: 22
  loop : -2.08 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 460 
 TYR   0.034   0.001   TYR A 199 
 PHE   0.010   0.001   PHE A 523 
 TRP   0.036   0.002   TRP A 477 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6791)
  covalent geometry    : angle       0.60041 ( 9230)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       0.56046 (   12)
  hydrogen bonds       : bond        0.09981 (  281)
  hydrogen bonds       : angle       5.14367 (  810)
  link_ALPHA1-3        : bond        0.00481 (    1)
  link_ALPHA1-3        : angle       1.68575 (    3)
  link_ALPHA1-6        : bond        0.00538 (    1)
  link_ALPHA1-6        : angle       1.50007 (    3)
  link_BETA1-4         : bond        0.00438 (    6)
  link_BETA1-4         : angle       1.33185 (   18)
  link_NAG-ASN         : bond        0.01011 (    6)
  link_NAG-ASN         : angle       3.69641 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8630 (m) cc_final: 0.7945 (t)
REVERT: A   72 PHE cc_start: 0.8554 (t80) cc_final: 0.8227 (t80)
REVERT: A   83 TYR cc_start: 0.6487 (m-80) cc_final: 0.4755 (m-80)
REVERT: A   97 LEU cc_start: 0.8731 (tp) cc_final: 0.8522 (tp)
REVERT: A  189 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8309 (mm-30)
REVERT: A  207 TYR cc_start: 0.7867 (m-80) cc_final: 0.7535 (m-80)
REVERT: A  232 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: A  265 HIS cc_start: 0.7867 (p90) cc_final: 0.7666 (p90)
REVERT: A  279 TYR cc_start: 0.7245 (t80) cc_final: 0.6939 (t80)
REVERT: A  483 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7086 (mt-10)
REVERT: A  518 ARG cc_start: 0.6955 (ppt170) cc_final: 0.6306 (ppt170)
REVERT: A  557 MET cc_start: 0.8294 (tmm) cc_final: 0.8034 (ppp)
REVERT: B  347 PHE cc_start: 0.6552 (m-10) cc_final: 0.4936 (m-80)
REVERT: B  351 TYR cc_start: 0.6728 (t80) cc_final: 0.6398 (t80)
REVERT: B  353 TRP cc_start: 0.7597 (p-90) cc_final: 0.7166 (p-90)
REVERT: B  355 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7364 (mmm-85)
REVERT: B  442 ASP cc_start: 0.7889 (t70) cc_final: 0.7038 (p0)
REVERT: B  444 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7870 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0857
  time to fit residues: 20.8702
Evaluate side-chains
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 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 = 0.4044 r_free = 0.4044 target = 0.149880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.128617 restraints weight = 18364.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.132360 restraints weight = 13430.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.133480 restraints weight = 8656.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.134137 restraints weight = 6931.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.135502 restraints weight = 6244.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6811  Z= 0.147
  Angle     :  0.650  11.373   9284  Z= 0.324
  Chirality :  0.045   0.265   1003
  Planarity :  0.005   0.041   1173
  Dihedral  : 11.325  75.633   1143
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.17 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.31), residues: 786
  helix:  1.68 (0.28), residues: 366
  sheet:  0.46 (0.91), residues: 32
  loop : -2.06 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 346 
 TYR   0.015   0.002   TYR B 453 
 PHE   0.021   0.001   PHE B 464 
 TRP   0.016   0.001   TRP A 461 
 HIS   0.010   0.002   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6791)
  covalent geometry    : angle       0.61561 ( 9230)
  SS BOND              : bond        0.00472 (    6)
  SS BOND              : angle       2.20781 (   12)
  hydrogen bonds       : bond        0.04344 (  281)
  hydrogen bonds       : angle       4.92049 (  810)
  link_ALPHA1-3        : bond        0.01213 (    1)
  link_ALPHA1-3        : angle       3.22826 (    3)
  link_ALPHA1-6        : bond        0.00441 (    1)
  link_ALPHA1-6        : angle       2.11753 (    3)
  link_BETA1-4         : bond        0.00712 (    6)
  link_BETA1-4         : angle       1.84609 (   18)
  link_NAG-ASN         : bond        0.01068 (    6)
  link_NAG-ASN         : angle       3.78361 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8752 (m) cc_final: 0.7853 (t)
REVERT: A   72 PHE cc_start: 0.8427 (t80) cc_final: 0.8078 (t80)
REVERT: A  207 TYR cc_start: 0.7808 (m-80) cc_final: 0.7546 (m-80)
REVERT: A  232 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7933 (mm-30)
REVERT: A  265 HIS cc_start: 0.7869 (p90) cc_final: 0.7002 (p90)
REVERT: A  474 MET cc_start: 0.8067 (mmm) cc_final: 0.7807 (mmm)
REVERT: A  483 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7294 (mt-10)
REVERT: B  351 TYR cc_start: 0.7056 (t80) cc_final: 0.6588 (t80)
REVERT: B  353 TRP cc_start: 0.7560 (p-90) cc_final: 0.6943 (p-90)
REVERT: B  442 ASP cc_start: 0.7978 (t70) cc_final: 0.7116 (p0)
REVERT: B  444 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7811 (mmtt)
REVERT: B  457 ARG cc_start: 0.7741 (tmt-80) cc_final: 0.7094 (tmt-80)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0761
  time to fit residues: 14.8254
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0980
   chunk 18 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0770
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.150047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.129357 restraints weight = 18367.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.133132 restraints weight = 13452.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.134230 restraints weight = 8472.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.134999 restraints weight = 6650.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.135621 restraints weight = 6206.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   6811  Z= 0.129
  Angle     :  0.633  12.389   9284  Z= 0.311
  Chirality :  0.044   0.259   1003
  Planarity :  0.004   0.040   1173
  Dihedral  :  9.632  65.626   1143
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.31), residues: 786
  helix:  1.62 (0.28), residues: 366
  sheet:  0.29 (0.90), residues: 32
  loop : -2.03 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 357 
 TYR   0.018   0.001   TYR B 453 
 PHE   0.016   0.001   PHE A 512 
 TRP   0.016   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6791)
  covalent geometry    : angle       0.59897 ( 9230)
  SS BOND              : bond        0.01141 (    6)
  SS BOND              : angle       2.28446 (   12)
  hydrogen bonds       : bond        0.04280 (  281)
  hydrogen bonds       : angle       4.77628 (  810)
  link_ALPHA1-3        : bond        0.01284 (    1)
  link_ALPHA1-3        : angle       2.49520 (    3)
  link_ALPHA1-6        : bond        0.00768 (    1)
  link_ALPHA1-6        : angle       2.19379 (    3)
  link_BETA1-4         : bond        0.00578 (    6)
  link_BETA1-4         : angle       1.89206 (   18)
  link_NAG-ASN         : bond        0.01031 (    6)
  link_NAG-ASN         : angle       3.72391 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8609 (m) cc_final: 0.7570 (t)
REVERT: A   83 TYR cc_start: 0.6338 (m-80) cc_final: 0.5605 (m-80)
REVERT: A  207 TYR cc_start: 0.7741 (m-80) cc_final: 0.7471 (m-80)
REVERT: A  232 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8027 (mt-10)
REVERT: A  355 ASP cc_start: 0.8001 (t0) cc_final: 0.7656 (p0)
REVERT: A  406 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5914 (mt-10)
REVERT: A  483 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7320 (mt-10)
REVERT: A  589 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7592 (mt-10)
REVERT: B  351 TYR cc_start: 0.6983 (t80) cc_final: 0.6574 (t80)
REVERT: B  355 ARG cc_start: 0.7421 (tpp80) cc_final: 0.6681 (mmm-85)
REVERT: B  405 ASN cc_start: 0.7120 (p0) cc_final: 0.6813 (p0)
REVERT: B  409 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7019 (mt0)
REVERT: B  442 ASP cc_start: 0.7488 (t70) cc_final: 0.7181 (p0)
REVERT: B  444 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7843 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0851
  time to fit residues: 16.9181
Evaluate side-chains
  115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 53 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0870
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.8560

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.151290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.130147 restraints weight = 18747.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.133900 restraints weight = 13192.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.135138 restraints weight = 8782.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.135859 restraints weight = 7058.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.136723 restraints weight = 6206.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6811  Z= 0.132
  Angle     :  0.642  11.114   9284  Z= 0.316
  Chirality :  0.044   0.261   1003
  Planarity :  0.004   0.037   1173
  Dihedral  :  8.719  59.448   1143
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.31), residues: 786
  helix:  1.56 (0.28), residues: 368
  sheet: -0.09 (0.85), residues: 32
  loop : -2.12 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 355 
 TYR   0.018   0.002   TYR B 453 
 PHE   0.017   0.001   PHE B 464 
 TRP   0.014   0.001   TRP A 477 
 HIS   0.007   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6791)
  covalent geometry    : angle       0.61029 ( 9230)
  SS BOND              : bond        0.00909 (    6)
  SS BOND              : angle       1.83121 (   12)
  hydrogen bonds       : bond        0.04237 (  281)
  hydrogen bonds       : angle       4.75268 (  810)
  link_ALPHA1-3        : bond        0.01220 (    1)
  link_ALPHA1-3        : angle       2.69148 (    3)
  link_ALPHA1-6        : bond        0.00761 (    1)
  link_ALPHA1-6        : angle       2.24601 (    3)
  link_BETA1-4         : bond        0.00578 (    6)
  link_BETA1-4         : angle       1.86945 (   18)
  link_NAG-ASN         : bond        0.01008 (    6)
  link_NAG-ASN         : angle       3.69597 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8671 (m) cc_final: 0.7595 (t)
REVERT: A   72 PHE cc_start: 0.8480 (t80) cc_final: 0.8075 (t80)
REVERT: A  207 TYR cc_start: 0.7748 (m-80) cc_final: 0.7516 (m-80)
REVERT: A  222 LEU cc_start: 0.9306 (mt) cc_final: 0.9017 (mt)
REVERT: A  355 ASP cc_start: 0.8007 (t0) cc_final: 0.7708 (p0)
REVERT: A  406 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5941 (mt-10)
REVERT: A  418 LEU cc_start: 0.9128 (mt) cc_final: 0.8915 (tp)
REVERT: A  483 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7318 (mt-10)
REVERT: A  589 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7621 (mt-10)
REVERT: B  351 TYR cc_start: 0.7215 (t80) cc_final: 0.6900 (t80)
REVERT: B  353 TRP cc_start: 0.7357 (p-90) cc_final: 0.7034 (p-90)
REVERT: B  442 ASP cc_start: 0.7653 (t70) cc_final: 0.7226 (p0)
REVERT: B  444 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7819 (mmtt)
REVERT: B  457 ARG cc_start: 0.7773 (tmt-80) cc_final: 0.7092 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0790
  time to fit residues: 16.1402
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0030
   chunk 60 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 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 = 0.4060 r_free = 0.4060 target = 0.151528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.130584 restraints weight = 18529.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.134372 restraints weight = 13306.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.135698 restraints weight = 8737.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.136439 restraints weight = 7061.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.137546 restraints weight = 6195.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6811  Z= 0.127
  Angle     :  0.641  10.958   9284  Z= 0.317
  Chirality :  0.044   0.266   1003
  Planarity :  0.004   0.038   1173
  Dihedral  :  8.159  52.309   1143
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.31), residues: 786
  helix:  1.45 (0.28), residues: 367
  sheet: -0.19 (0.86), residues: 32
  loop : -2.14 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 355 
 TYR   0.026   0.002   TYR A  83 
 PHE   0.020   0.001   PHE B 377 
 TRP   0.034   0.001   TRP A 477 
 HIS   0.006   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6791)
  covalent geometry    : angle       0.61133 ( 9230)
  SS BOND              : bond        0.00749 (    6)
  SS BOND              : angle       1.46152 (   12)
  hydrogen bonds       : bond        0.04273 (  281)
  hydrogen bonds       : angle       4.70137 (  810)
  link_ALPHA1-3        : bond        0.01369 (    1)
  link_ALPHA1-3        : angle       2.48251 (    3)
  link_ALPHA1-6        : bond        0.00987 (    1)
  link_ALPHA1-6        : angle       2.12497 (    3)
  link_BETA1-4         : bond        0.00605 (    6)
  link_BETA1-4         : angle       1.91736 (   18)
  link_NAG-ASN         : bond        0.01119 (    6)
  link_NAG-ASN         : angle       3.66344 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8620 (m) cc_final: 0.7577 (t)
REVERT: A   72 PHE cc_start: 0.8311 (t80) cc_final: 0.7971 (t80)
REVERT: A  181 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7674 (mt-10)
REVERT: A  186 LEU cc_start: 0.9330 (mt) cc_final: 0.9095 (mt)
REVERT: A  189 GLU cc_start: 0.8729 (pt0) cc_final: 0.8253 (mm-30)
REVERT: A  207 TYR cc_start: 0.7668 (m-80) cc_final: 0.7423 (m-80)
REVERT: A  222 LEU cc_start: 0.9310 (mt) cc_final: 0.9023 (mt)
REVERT: A  355 ASP cc_start: 0.8001 (t0) cc_final: 0.7682 (p0)
REVERT: A  406 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5934 (mt-10)
REVERT: A  477 TRP cc_start: 0.7674 (t-100) cc_final: 0.6854 (t-100)
REVERT: A  589 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7644 (mt-10)
REVERT: A  592 PHE cc_start: 0.7811 (t80) cc_final: 0.7580 (t80)
REVERT: B  351 TYR cc_start: 0.7137 (t80) cc_final: 0.6816 (t80)
REVERT: B  353 TRP cc_start: 0.7317 (p-90) cc_final: 0.7055 (p-90)
REVERT: B  442 ASP cc_start: 0.7653 (t70) cc_final: 0.7221 (p0)
REVERT: B  457 ARG cc_start: 0.7696 (tmt-80) cc_final: 0.7440 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0883
  time to fit residues: 17.3988
Evaluate side-chains
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0370
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 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 = 0.4066 r_free = 0.4066 target = 0.152317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.131586 restraints weight = 18344.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.135553 restraints weight = 13446.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.136770 restraints weight = 8498.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.137605 restraints weight = 6668.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.138406 restraints weight = 6077.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6811  Z= 0.120
  Angle     :  0.625  10.797   9284  Z= 0.310
  Chirality :  0.043   0.271   1003
  Planarity :  0.004   0.039   1173
  Dihedral  :  7.616  58.533   1143
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.31), residues: 786
  helix:  1.47 (0.28), residues: 367
  sheet: -0.34 (0.87), residues: 32
  loop : -2.12 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 357 
 TYR   0.020   0.001   TYR A  83 
 PHE   0.016   0.001   PHE B 464 
 TRP   0.037   0.001   TRP A 477 
 HIS   0.008   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6791)
  covalent geometry    : angle       0.59735 ( 9230)
  SS BOND              : bond        0.00665 (    6)
  SS BOND              : angle       1.23546 (   12)
  hydrogen bonds       : bond        0.04162 (  281)
  hydrogen bonds       : angle       4.68163 (  810)
  link_ALPHA1-3        : bond        0.01223 (    1)
  link_ALPHA1-3        : angle       2.81345 (    3)
  link_ALPHA1-6        : bond        0.01140 (    1)
  link_ALPHA1-6        : angle       1.35976 (    3)
  link_BETA1-4         : bond        0.00564 (    6)
  link_BETA1-4         : angle       1.68763 (   18)
  link_NAG-ASN         : bond        0.00982 (    6)
  link_NAG-ASN         : angle       3.57898 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.8053 (t80) cc_final: 0.7834 (t80)
REVERT: A   44 SER cc_start: 0.8653 (m) cc_final: 0.7842 (t)
REVERT: A   72 PHE cc_start: 0.8496 (t80) cc_final: 0.8083 (t80)
REVERT: A  181 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7669 (mt-10)
REVERT: A  186 LEU cc_start: 0.9322 (mt) cc_final: 0.9058 (mt)
REVERT: A  189 GLU cc_start: 0.8701 (pt0) cc_final: 0.8204 (mm-30)
REVERT: A  207 TYR cc_start: 0.7651 (m-80) cc_final: 0.7355 (m-80)
REVERT: A  222 LEU cc_start: 0.9285 (mt) cc_final: 0.9007 (mt)
REVERT: A  355 ASP cc_start: 0.7973 (t0) cc_final: 0.7653 (p0)
REVERT: A  589 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7629 (mt-10)
REVERT: B  351 TYR cc_start: 0.7159 (t80) cc_final: 0.6832 (t80)
REVERT: B  353 TRP cc_start: 0.7335 (p-90) cc_final: 0.7135 (p-90)
REVERT: B  442 ASP cc_start: 0.7683 (t70) cc_final: 0.7164 (p0)
REVERT: B  457 ARG cc_start: 0.7611 (tmt-80) cc_final: 0.7264 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0830
  time to fit residues: 16.0712
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 51 optimal weight:    0.2980
   chunk 44 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0570
   chunk 47 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS
A 265 HIS
** B 474 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.152594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.132129 restraints weight = 18444.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.136239 restraints weight = 13619.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.137110 restraints weight = 8592.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.137722 restraints weight = 6797.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.139419 restraints weight = 6258.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6811  Z= 0.119
  Angle     :  0.618  10.712   9284  Z= 0.307
  Chirality :  0.043   0.275   1003
  Planarity :  0.004   0.041   1173
  Dihedral  :  6.868  48.133   1143
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.31), residues: 786
  helix:  1.45 (0.28), residues: 370
  sheet: -0.45 (0.88), residues: 32
  loop : -2.09 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 355 
 TYR   0.018   0.001   TYR B 453 
 PHE   0.017   0.001   PHE A 592 
 TRP   0.033   0.001   TRP A 477 
 HIS   0.010   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6791)
  covalent geometry    : angle       0.59117 ( 9230)
  SS BOND              : bond        0.00625 (    6)
  SS BOND              : angle       1.21293 (   12)
  hydrogen bonds       : bond        0.04060 (  281)
  hydrogen bonds       : angle       4.63220 (  810)
  link_ALPHA1-3        : bond        0.01167 (    1)
  link_ALPHA1-3        : angle       3.06463 (    3)
  link_ALPHA1-6        : bond        0.01378 (    1)
  link_ALPHA1-6        : angle       1.20729 (    3)
  link_BETA1-4         : bond        0.00602 (    6)
  link_BETA1-4         : angle       1.61336 (   18)
  link_NAG-ASN         : bond        0.00949 (    6)
  link_NAG-ASN         : angle       3.54334 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8658 (m) cc_final: 0.7852 (t)
REVERT: A   72 PHE cc_start: 0.8497 (t80) cc_final: 0.8090 (t80)
REVERT: A  181 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7513 (mt-10)
REVERT: A  186 LEU cc_start: 0.9300 (mt) cc_final: 0.9082 (mt)
REVERT: A  189 GLU cc_start: 0.8717 (pt0) cc_final: 0.8232 (mm-30)
REVERT: A  207 TYR cc_start: 0.7667 (m-80) cc_final: 0.7381 (m-80)
REVERT: A  222 LEU cc_start: 0.9301 (mt) cc_final: 0.9023 (mt)
REVERT: A  355 ASP cc_start: 0.7949 (t0) cc_final: 0.7649 (p0)
REVERT: A  589 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7650 (mt-10)
REVERT: A  592 PHE cc_start: 0.7824 (t80) cc_final: 0.7540 (t80)
REVERT: B  351 TYR cc_start: 0.7180 (t80) cc_final: 0.6790 (t80)
REVERT: B  442 ASP cc_start: 0.7605 (t70) cc_final: 0.7180 (p0)
REVERT: B  457 ARG cc_start: 0.7537 (tmt-80) cc_final: 0.7192 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0856
  time to fit residues: 15.7776
Evaluate side-chains
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.147690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.126961 restraints weight = 18373.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.130006 restraints weight = 13518.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.131496 restraints weight = 9159.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.132315 restraints weight = 7121.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.133380 restraints weight = 6414.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6811  Z= 0.183
  Angle     :  0.708  10.784   9284  Z= 0.355
  Chirality :  0.046   0.275   1003
  Planarity :  0.005   0.044   1173
  Dihedral  :  7.368  50.383   1143
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.43 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.30), residues: 786
  helix:  1.29 (0.28), residues: 364
  sheet: -0.95 (0.81), residues: 32
  loop : -2.22 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.035   0.002   TYR B 453 
 PHE   0.017   0.002   PHE A 592 
 TRP   0.031   0.002   TRP A 477 
 HIS   0.010   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6791)
  covalent geometry    : angle       0.68124 ( 9230)
  SS BOND              : bond        0.00676 (    6)
  SS BOND              : angle       1.22346 (   12)
  hydrogen bonds       : bond        0.04715 (  281)
  hydrogen bonds       : angle       4.96717 (  810)
  link_ALPHA1-3        : bond        0.01196 (    1)
  link_ALPHA1-3        : angle       2.71002 (    3)
  link_ALPHA1-6        : bond        0.01031 (    1)
  link_ALPHA1-6        : angle       1.02145 (    3)
  link_BETA1-4         : bond        0.00675 (    6)
  link_BETA1-4         : angle       1.92334 (   18)
  link_NAG-ASN         : bond        0.01012 (    6)
  link_NAG-ASN         : angle       3.78582 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7595 (mt-10)
REVERT: A  186 LEU cc_start: 0.9300 (mt) cc_final: 0.9042 (mt)
REVERT: A  189 GLU cc_start: 0.8744 (pt0) cc_final: 0.8130 (mm-30)
REVERT: A  207 TYR cc_start: 0.7820 (m-80) cc_final: 0.7554 (m-80)
REVERT: A  483 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: A  589 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7656 (mt-10)
REVERT: A  592 PHE cc_start: 0.7860 (t80) cc_final: 0.7648 (t80)
REVERT: B  351 TYR cc_start: 0.7393 (t80) cc_final: 0.6931 (t80)
REVERT: B  457 ARG cc_start: 0.7705 (tmt-80) cc_final: 0.7210 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0812
  time to fit residues: 15.1374
Evaluate side-chains
  105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    0.6980
   chunk 58 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.149468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.128906 restraints weight = 18593.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.132214 restraints weight = 12822.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.132969 restraints weight = 8887.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.133925 restraints weight = 7225.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.134964 restraints weight = 6299.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6811  Z= 0.146
  Angle     :  0.680  10.812   9284  Z= 0.339
  Chirality :  0.045   0.282   1003
  Planarity :  0.004   0.043   1173
  Dihedral  :  7.129  52.814   1143
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.30), residues: 786
  helix:  1.32 (0.28), residues: 356
  sheet: -0.50 (0.80), residues: 30
  loop : -2.21 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 357 
 TYR   0.024   0.002   TYR B 453 
 PHE   0.033   0.002   PHE B 392 
 TRP   0.029   0.002   TRP A 477 
 HIS   0.009   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6791)
  covalent geometry    : angle       0.65340 ( 9230)
  SS BOND              : bond        0.00684 (    6)
  SS BOND              : angle       1.22693 (   12)
  hydrogen bonds       : bond        0.04594 (  281)
  hydrogen bonds       : angle       4.87546 (  810)
  link_ALPHA1-3        : bond        0.01254 (    1)
  link_ALPHA1-3        : angle       2.74511 (    3)
  link_ALPHA1-6        : bond        0.01054 (    1)
  link_ALPHA1-6        : angle       1.21173 (    3)
  link_BETA1-4         : bond        0.00601 (    6)
  link_BETA1-4         : angle       1.74173 (   18)
  link_NAG-ASN         : bond        0.01002 (    6)
  link_NAG-ASN         : angle       3.69916 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8564 (m) cc_final: 0.7762 (t)
REVERT: A   72 PHE cc_start: 0.8416 (t80) cc_final: 0.8048 (t80)
REVERT: A  152 MET cc_start: 0.8282 (mmp) cc_final: 0.7807 (mmm)
REVERT: A  181 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7621 (mt-10)
REVERT: A  186 LEU cc_start: 0.9332 (mt) cc_final: 0.9116 (mt)
REVERT: A  189 GLU cc_start: 0.8759 (pt0) cc_final: 0.8208 (mm-30)
REVERT: A  222 LEU cc_start: 0.9294 (mt) cc_final: 0.9037 (mt)
REVERT: A  589 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7654 (mt-10)
REVERT: A  592 PHE cc_start: 0.7828 (t80) cc_final: 0.7611 (t80)
REVERT: B  351 TYR cc_start: 0.7085 (t80) cc_final: 0.6747 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0831
  time to fit residues: 14.5343
Evaluate side-chains
  99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
** A  58 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 = 0.4046 r_free = 0.4046 target = 0.150176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.129798 restraints weight = 18258.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.133326 restraints weight = 12861.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.134154 restraints weight = 8608.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.135034 restraints weight = 6985.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.136117 restraints weight = 6159.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6811  Z= 0.132
  Angle     :  0.663  10.826   9284  Z= 0.330
  Chirality :  0.045   0.279   1003
  Planarity :  0.004   0.042   1173
  Dihedral  :  6.864  52.285   1143
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.30), residues: 786
  helix:  1.48 (0.28), residues: 354
  sheet: -0.43 (0.83), residues: 32
  loop : -2.18 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 357 
 TYR   0.022   0.002   TYR B 453 
 PHE   0.020   0.001   PHE A  32 
 TRP   0.030   0.002   TRP A 477 
 HIS   0.010   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6791)
  covalent geometry    : angle       0.63697 ( 9230)
  SS BOND              : bond        0.00627 (    6)
  SS BOND              : angle       1.16275 (   12)
  hydrogen bonds       : bond        0.04406 (  281)
  hydrogen bonds       : angle       4.80194 (  810)
  link_ALPHA1-3        : bond        0.01153 (    1)
  link_ALPHA1-3        : angle       2.58042 (    3)
  link_ALPHA1-6        : bond        0.01009 (    1)
  link_ALPHA1-6        : angle       1.33800 (    3)
  link_BETA1-4         : bond        0.00559 (    6)
  link_BETA1-4         : angle       1.71456 (   18)
  link_NAG-ASN         : bond        0.00968 (    6)
  link_NAG-ASN         : angle       3.67287 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8605 (m) cc_final: 0.7684 (t)
REVERT: A   72 PHE cc_start: 0.8382 (t80) cc_final: 0.8028 (t80)
REVERT: A  181 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7573 (mt-10)
REVERT: A  186 LEU cc_start: 0.9332 (mt) cc_final: 0.9114 (mt)
REVERT: A  189 GLU cc_start: 0.8729 (pt0) cc_final: 0.8185 (mm-30)
REVERT: A  222 LEU cc_start: 0.9245 (mt) cc_final: 0.9011 (mt)
REVERT: A  355 ASP cc_start: 0.8074 (t0) cc_final: 0.7448 (p0)
REVERT: A  589 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7636 (mt-10)
REVERT: A  592 PHE cc_start: 0.7794 (t80) cc_final: 0.7592 (t80)
REVERT: B  351 TYR cc_start: 0.7110 (t80) cc_final: 0.6754 (t80)
REVERT: B  457 ARG cc_start: 0.7809 (tmt-80) cc_final: 0.7313 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0813
  time to fit residues: 13.7274
Evaluate side-chains
  98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.0060
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 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 = 0.4054 r_free = 0.4054 target = 0.150755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.130709 restraints weight = 18582.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.134117 restraints weight = 12885.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.134646 restraints weight = 8964.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.135559 restraints weight = 7205.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.137176 restraints weight = 6254.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6811  Z= 0.122
  Angle     :  0.646  10.779   9284  Z= 0.321
  Chirality :  0.044   0.282   1003
  Planarity :  0.004   0.045   1173
  Dihedral  :  6.604  52.040   1143
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.30), residues: 786
  helix:  1.51 (0.28), residues: 355
  sheet: -0.30 (0.84), residues: 32
  loop : -2.18 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 355 
 TYR   0.025   0.002   TYR A 279 
 PHE   0.022   0.001   PHE A  32 
 TRP   0.031   0.001   TRP A 477 
 HIS   0.010   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6791)
  covalent geometry    : angle       0.62003 ( 9230)
  SS BOND              : bond        0.00615 (    6)
  SS BOND              : angle       1.14218 (   12)
  hydrogen bonds       : bond        0.04314 (  281)
  hydrogen bonds       : angle       4.78775 (  810)
  link_ALPHA1-3        : bond        0.01046 (    1)
  link_ALPHA1-3        : angle       2.45892 (    3)
  link_ALPHA1-6        : bond        0.01023 (    1)
  link_ALPHA1-6        : angle       1.44855 (    3)
  link_BETA1-4         : bond        0.00543 (    6)
  link_BETA1-4         : angle       1.65653 (   18)
  link_NAG-ASN         : bond        0.00944 (    6)
  link_NAG-ASN         : angle       3.61920 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1243.43 seconds
wall clock time: 22 minutes 13.64 seconds (1333.64 seconds total)