Starting phenix.real_space_refine
on Fri Feb 14 20:40:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iu1_60886/02_2025/9iu1_60886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iu1_60886/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2025/9iu1_60886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2025/9iu1_60886.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2025/9iu1_60886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2025/9iu1_60886.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.82, per 1000 atoms: 0.73
  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: 1.91
  Conformation dependent library (CDL) restraints added in 960.0 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: 0.66
  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: 1.55

  Time building geometry restraints manager: 2.19 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:             3.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.210
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.000
-------------------------------------------------------------------------------
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   6791  Z= 0.207
  Angle     :  0.600   6.532   9230  Z= 0.293
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (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
 TRP   0.036   0.002   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.010   0.001   PHE A 523 
 TYR   0.034   0.001   TYR A 199 
 ARG   0.002   0.000   ARG A 460 

*********************** 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  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8630 (m) cc_final: 0.7949 (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: 0.4803 (m-80)
REVERT: A  189 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8306 (mm-30)
REVERT: A  207 TYR cc_start: 0.7867 (m-80) cc_final: 0.7536 (m-80)
REVERT: A  232 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7857 (mm-30)
REVERT: A  279 TYR cc_start: 0.7245 (t80) cc_final: 0.6961 (t80)
REVERT: A  483 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7089 (mt-10)
REVERT: A  518 ARG cc_start: 0.6955 (ppt170) cc_final: 0.6304 (ppt170)
REVERT: A  557 MET cc_start: 0.8294 (tmm) cc_final: 0.8035 (ppp)
REVERT: B  347 PHE cc_start: 0.6552 (m-10) cc_final: 0.4919 (m-80)
REVERT: B  351 TYR cc_start: 0.6728 (t80) cc_final: 0.6407 (t80)
REVERT: B  353 TRP cc_start: 0.7597 (p-90) cc_final: 0.7029 (p-90)
REVERT: B  355 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7360 (mmm-85)
REVERT: B  442 ASP cc_start: 0.7889 (t70) cc_final: 0.7041 (p0)
REVERT: B  444 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7875 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1974
  time to fit residues: 47.2576
Evaluate side-chains
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.1980
   chunk 23 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    2.0388

-------------------------------------------------------------------------------
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  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.146528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.125553 restraints weight = 18049.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.128582 restraints weight = 13184.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.130063 restraints weight = 8934.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6791  Z= 0.292
  Angle     :  0.680   8.289   9230  Z= 0.350
  Chirality :  0.047   0.269   1003
  Planarity :  0.005   0.044   1173
  Dihedral  : 11.337  72.677   1143
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.81 %
    Favored  : 89.19 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.90 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.31), residues: 786
  helix:  1.41 (0.28), residues: 371
  sheet:  0.04 (0.89), residues: 32
  loop : -2.21 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 461 
 HIS   0.009   0.002   HIS A 228 
 PHE   0.019   0.002   PHE B 464 
 TYR   0.023   0.002   TYR B 453 
 ARG   0.003   0.001   ARG B 346 

*********************** 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
  141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.743 
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: 0.8635 (m) cc_final: 0.7649 (t)
REVERT: A   72 PHE cc_start: 0.8524 (t80) cc_final: 0.8183 (t80)
REVERT: A  207 TYR cc_start: 0.7930 (m-80) cc_final: 0.7650 (m-80)
REVERT: A  265 HIS cc_start: 0.7783 (p90) cc_final: 0.7199 (p90)
REVERT: A  474 MET cc_start: 0.8177 (mmm) cc_final: 0.7919 (mmm)
REVERT: A  483 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7346 (mt-10)
REVERT: B  351 TYR cc_start: 0.7091 (t80) cc_final: 0.6575 (t80)
REVERT: B  353 TRP cc_start: 0.7671 (p-90) cc_final: 0.6720 (p-90)
REVERT: B  442 ASP cc_start: 0.8042 (t70) cc_final: 0.7183 (p0)
REVERT: B  444 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7867 (mmtt)
REVERT: B  457 ARG cc_start: 0.7862 (tmt-80) cc_final: 0.7162 (tmt-80)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2013
  time to fit residues: 38.3500
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 401 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 = 0.3994 r_free = 0.3994 target = 0.146287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.125403 restraints weight = 18744.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.128760 restraints weight = 13143.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129513 restraints weight = 8968.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   6791  Z= 0.254
  Angle     :  0.659  12.500   9230  Z= 0.336
  Chirality :  0.046   0.266   1003
  Planarity :  0.005   0.042   1173
  Dihedral  : 10.228  62.477   1143
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.30), residues: 786
  helix:  1.28 (0.28), residues: 371
  sheet: -0.21 (0.91), residues: 32
  loop : -2.25 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.022   0.002   PHE B 392 
 TYR   0.028   0.002   TYR B 453 
 ARG   0.004   0.000   ARG B 355 

*********************** 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
  141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8687 (m) cc_final: 0.7683 (t)
REVERT: A   72 PHE cc_start: 0.8419 (t80) cc_final: 0.8111 (t80)
REVERT: A   82 MET cc_start: 0.7714 (ptp) cc_final: 0.7489 (ptt)
REVERT: A   97 LEU cc_start: 0.8790 (tp) cc_final: 0.8351 (tp)
REVERT: A  207 TYR cc_start: 0.7863 (m-80) cc_final: 0.7593 (m-80)
REVERT: A  232 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7977 (mt-10)
REVERT: A  418 LEU cc_start: 0.8974 (mm) cc_final: 0.8634 (tp)
REVERT: A  483 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7363 (mt-10)
REVERT: B  351 TYR cc_start: 0.7084 (t80) cc_final: 0.6602 (t80)
REVERT: B  353 TRP cc_start: 0.7833 (p-90) cc_final: 0.7224 (p-90)
REVERT: B  355 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7086 (tpp80)
REVERT: B  387 LEU cc_start: 0.8812 (tp) cc_final: 0.8611 (tp)
REVERT: B  405 ASN cc_start: 0.7132 (p0) cc_final: 0.6818 (p0)
REVERT: B  409 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7134 (mt0)
REVERT: B  423 TYR cc_start: 0.7712 (t80) cc_final: 0.7172 (t80)
REVERT: B  442 ASP cc_start: 0.7669 (t70) cc_final: 0.7148 (p0)
REVERT: B  444 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7869 (mmtt)
REVERT: B  457 ARG cc_start: 0.7768 (tmt-80) cc_final: 0.7084 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1880
  time to fit residues: 35.0312
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 102 GLN
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.147719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.126044 restraints weight = 18759.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.129425 restraints weight = 13494.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.130901 restraints weight = 9006.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6791  Z= 0.238
  Angle     :  0.653  10.497   9230  Z= 0.336
  Chirality :  0.046   0.270   1003
  Planarity :  0.005   0.063   1173
  Dihedral  :  9.349  59.234   1143
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.30), residues: 786
  helix:  1.19 (0.27), residues: 371
  sheet:  0.23 (0.91), residues: 32
  loop : -2.31 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 353 
 HIS   0.008   0.001   HIS A 228 
 PHE   0.021   0.002   PHE B 400 
 TYR   0.024   0.002   TYR B 453 
 ARG   0.004   0.000   ARG B 508 

*********************** 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
  139 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.703 
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: 0.8496 (m) cc_final: 0.7678 (t)
REVERT: A  117 ASN cc_start: 0.8238 (m-40) cc_final: 0.7422 (t0)
REVERT: A  207 TYR cc_start: 0.7915 (m-80) cc_final: 0.7649 (m-80)
REVERT: A  406 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6192 (mt-10)
REVERT: A  483 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: B  351 TYR cc_start: 0.7123 (t80) cc_final: 0.6696 (t80)
REVERT: B  442 ASP cc_start: 0.7861 (t70) cc_final: 0.7246 (p0)
REVERT: B  444 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7908 (mmtt)
REVERT: B  457 ARG cc_start: 0.7808 (tmt-80) cc_final: 0.7067 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1918
  time to fit residues: 35.2334
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9742

-------------------------------------------------------------------------------
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
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.149293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.128160 restraints weight = 18448.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.132069 restraints weight = 13601.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.133172 restraints weight = 8691.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6791  Z= 0.192
  Angle     :  0.625   9.052   9230  Z= 0.321
  Chirality :  0.045   0.271   1003
  Planarity :  0.004   0.046   1173
  Dihedral  :  8.302  52.644   1143
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.30), residues: 786
  helix:  1.32 (0.28), residues: 369
  sheet:  0.36 (0.91), residues: 32
  loop : -2.25 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 477 
 HIS   0.007   0.001   HIS A 228 
 PHE   0.022   0.002   PHE B 377 
 TYR   0.024   0.002   TYR A  83 
 ARG   0.005   0.000   ARG B 357 

*********************** 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
  133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8643 (m) cc_final: 0.7957 (t)
REVERT: A  117 ASN cc_start: 0.8228 (m-40) cc_final: 0.7417 (t0)
REVERT: A  181 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7604 (mt-10)
REVERT: A  207 TYR cc_start: 0.7804 (m-80) cc_final: 0.7580 (m-80)
REVERT: A  418 LEU cc_start: 0.8889 (mm) cc_final: 0.8599 (tp)
REVERT: A  477 TRP cc_start: 0.7799 (t-100) cc_final: 0.7034 (t-100)
REVERT: A  589 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7685 (mt-10)
REVERT: B  351 TYR cc_start: 0.7033 (t80) cc_final: 0.6666 (t80)
REVERT: B  409 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7056 (mt0)
REVERT: B  423 TYR cc_start: 0.7238 (t80) cc_final: 0.7033 (t80)
REVERT: B  442 ASP cc_start: 0.7915 (t70) cc_final: 0.7248 (p0)
REVERT: B  444 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7891 (mmtt)
REVERT: B  457 ARG cc_start: 0.7598 (tmt-80) cc_final: 0.7352 (tmt-80)
REVERT: B  494 TYR cc_start: 0.6420 (m-80) cc_final: 0.6151 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1858
  time to fit residues: 33.1596
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0270
   chunk 11 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6840

-------------------------------------------------------------------------------
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
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.150588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.129777 restraints weight = 18249.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.133974 restraints weight = 13439.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.134663 restraints weight = 8473.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6791  Z= 0.170
  Angle     :  0.601   7.696   9230  Z= 0.310
  Chirality :  0.044   0.275   1003
  Planarity :  0.004   0.046   1173
  Dihedral  :  7.475  53.413   1143
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.30), residues: 786
  helix:  1.43 (0.28), residues: 366
  sheet:  0.42 (0.92), residues: 32
  loop : -2.22 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 477 
 HIS   0.008   0.001   HIS A 239 
 PHE   0.016   0.001   PHE A 592 
 TYR   0.018   0.001   TYR B 453 
 ARG   0.003   0.000   ARG B 357 

*********************** 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
  133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8700 (m) cc_final: 0.7898 (t)
REVERT: A   72 PHE cc_start: 0.8437 (t80) cc_final: 0.8150 (t80)
REVERT: A  181 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7668 (mt-10)
REVERT: A  355 ASP cc_start: 0.8113 (t0) cc_final: 0.7774 (p0)
REVERT: A  418 LEU cc_start: 0.8909 (mm) cc_final: 0.8624 (tp)
REVERT: A  589 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7621 (mt-10)
REVERT: B  351 TYR cc_start: 0.7064 (t80) cc_final: 0.6702 (t80)
REVERT: B  409 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7131 (mt0)
REVERT: B  442 ASP cc_start: 0.8064 (t70) cc_final: 0.7436 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1712
  time to fit residues: 31.0136
Evaluate side-chains
  101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 GLN
** 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 = 0.4048 r_free = 0.4048 target = 0.150451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.129618 restraints weight = 18513.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.133648 restraints weight = 13530.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.134505 restraints weight = 8633.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6791  Z= 0.179
  Angle     :  0.605   7.242   9230  Z= 0.313
  Chirality :  0.044   0.278   1003
  Planarity :  0.004   0.041   1173
  Dihedral  :  7.151  53.034   1143
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.31), residues: 786
  helix:  1.43 (0.28), residues: 367
  sheet:  0.16 (0.90), residues: 32
  loop : -2.14 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 477 
 HIS   0.008   0.001   HIS A 239 
 PHE   0.014   0.001   PHE A 512 
 TYR   0.031   0.002   TYR B 494 
 ARG   0.003   0.000   ARG B 357 

*********************** 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
  131 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8550 (m) cc_final: 0.7750 (t)
REVERT: A   72 PHE cc_start: 0.8389 (t80) cc_final: 0.8019 (t80)
REVERT: A  181 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7651 (mt-10)
REVERT: A  418 LEU cc_start: 0.8873 (mm) cc_final: 0.8617 (tp)
REVERT: A  589 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7672 (mt-10)
REVERT: A  592 PHE cc_start: 0.7826 (t80) cc_final: 0.7552 (t80)
REVERT: B  351 TYR cc_start: 0.7109 (t80) cc_final: 0.6763 (t80)
REVERT: B  442 ASP cc_start: 0.8127 (t70) cc_final: 0.7478 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1697
  time to fit residues: 30.3445
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0670
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 12 optimal weight:   30.0000
   overall best weight:    1.0722

-------------------------------------------------------------------------------
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 401 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 = 0.4045 r_free = 0.4045 target = 0.150135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.129563 restraints weight = 18536.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.133583 restraints weight = 13288.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.134470 restraints weight = 8381.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6791  Z= 0.189
  Angle     :  0.626   6.623   9230  Z= 0.325
  Chirality :  0.044   0.280   1003
  Planarity :  0.004   0.042   1173
  Dihedral  :  7.067  53.313   1143
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.30), residues: 786
  helix:  1.38 (0.28), residues: 361
  sheet: -0.29 (0.87), residues: 32
  loop : -2.16 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 477 
 HIS   0.007   0.001   HIS A 239 
 PHE   0.031   0.001   PHE A  32 
 TYR   0.025   0.002   TYR B 453 
 ARG   0.003   0.000   ARG B 357 

*********************** 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
  126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8460 (m) cc_final: 0.7588 (t)
REVERT: A  181 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7626 (mt-10)
REVERT: A  418 LEU cc_start: 0.8861 (mm) cc_final: 0.8568 (tp)
REVERT: A  589 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7647 (mt-10)
REVERT: B  351 TYR cc_start: 0.7133 (t80) cc_final: 0.6755 (t80)
REVERT: B  442 ASP cc_start: 0.8169 (t70) cc_final: 0.7228 (p0)
REVERT: B  444 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7891 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1719
  time to fit residues: 29.8403
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  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0000
   chunk 6 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0670
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5122

-------------------------------------------------------------------------------
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 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.152474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.131821 restraints weight = 18328.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.135398 restraints weight = 13035.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.136672 restraints weight = 8588.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6791  Z= 0.164
  Angle     :  0.616   7.597   9230  Z= 0.317
  Chirality :  0.044   0.283   1003
  Planarity :  0.004   0.041   1173
  Dihedral  :  6.711  54.297   1143
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.30), residues: 786
  helix:  1.40 (0.28), residues: 363
  sheet: -0.04 (0.85), residues: 32
  loop : -2.21 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 477 
 HIS   0.009   0.001   HIS A 345 
 PHE   0.027   0.002   PHE A  32 
 TYR   0.026   0.001   TYR B 453 
 ARG   0.003   0.000   ARG B 357 

*********************** 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  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8591 (m) cc_final: 0.7809 (t)
REVERT: A  181 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7515 (mt-10)
REVERT: A  418 LEU cc_start: 0.8856 (mm) cc_final: 0.8531 (tp)
REVERT: A  455 MET cc_start: 0.8263 (mmt) cc_final: 0.7822 (mmm)
REVERT: A  589 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7603 (mt-10)
REVERT: A  592 PHE cc_start: 0.7818 (t80) cc_final: 0.7530 (t80)
REVERT: B  351 TYR cc_start: 0.7005 (t80) cc_final: 0.6632 (t80)
REVERT: B  442 ASP cc_start: 0.8132 (t70) cc_final: 0.7153 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1644
  time to fit residues: 29.0406
Evaluate side-chains
  101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.150133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.129712 restraints weight = 18638.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.133439 restraints weight = 13548.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.134382 restraints weight = 8795.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6791  Z= 0.198
  Angle     :  0.646   7.610   9230  Z= 0.334
  Chirality :  0.045   0.280   1003
  Planarity :  0.004   0.046   1173
  Dihedral  :  6.746  53.240   1143
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.31), residues: 786
  helix:  1.45 (0.28), residues: 360
  sheet: -0.32 (0.84), residues: 32
  loop : -2.26 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 477 
 HIS   0.008   0.001   HIS A 239 
 PHE   0.026   0.002   PHE A  32 
 TYR   0.026   0.002   TYR B 453 
 ARG   0.003   0.000   ARG B 355 

********************** 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
  124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 SER cc_start: 0.8468 (m) cc_final: 0.7568 (t)
REVERT: A  181 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: A  418 LEU cc_start: 0.8839 (mm) cc_final: 0.8571 (tp)
REVERT: A  589 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7640 (mt-10)
REVERT: A  592 PHE cc_start: 0.7781 (t80) cc_final: 0.7477 (t80)
REVERT: B  351 TYR cc_start: 0.7165 (t80) cc_final: 0.6743 (t80)
REVERT: B  442 ASP cc_start: 0.8212 (t70) cc_final: 0.7238 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1671
  time to fit residues: 28.5485
Evaluate side-chains
  96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.0370
   chunk 23 optimal weight:    0.0070
   chunk 12 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0000
   chunk 65 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.1878

-------------------------------------------------------------------------------
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**
A 345 HIS
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4089 r_free = 0.4089 target = 0.153612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.132931 restraints weight = 18429.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.137083 restraints weight = 13642.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.138390 restraints weight = 8429.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6791  Z= 0.162
  Angle     :  0.627   7.453   9230  Z= 0.323
  Chirality :  0.044   0.286   1003
  Planarity :  0.004   0.043   1173
  Dihedral  :  6.392  54.860   1143
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.30), residues: 786
  helix:  1.36 (0.28), residues: 363
  sheet: -0.01 (0.83), residues: 32
  loop : -2.21 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 353 
 HIS   0.008   0.001   HIS A 239 
 PHE   0.023   0.001   PHE A  32 
 TYR   0.025   0.001   TYR A 279 
 ARG   0.011   0.001   ARG A 460 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2162.25 seconds
wall clock time: 39 minutes 38.72 seconds (2378.72 seconds total)