Starting phenix.real_space_refine
on Fri Aug 22 18:37:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hio_34824/08_2025/8hio_34824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hio_34824/08_2025/8hio_34824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2025/8hio_34824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2025/8hio_34824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2025/8hio_34824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2025/8hio_34824.cif"
  }
  resolution = 3.73
  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
-------------------------------------------------------------------------------
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=   0.012 sd=   0.211
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      47      5.49       5
     Mg      1      5.21       5
     S      21      5.16       5
     C    3952      2.51       5
     N    1281      2.21       5
     O    1378      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6681
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 1019
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 1019
          Classifications: {'RNA': 47}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 15, 'rna3p': 31}
    Chain: "A"
      Number of atoms: 4436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 567, 4436
          Classifications: {'peptide': 567}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 543}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1224
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 3, 'TRANS': 148}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5151  SG  CYS A 552     106.496  33.507  50.395  1.00185.32           S
  ATOM   5284  SG  CYS A 569     106.415  36.312  50.252  1.00190.90           S
  ATOM   5302  SG  CYS A 572     107.743  36.523  47.525  1.00196.84           S

  Time building chain proxies: 1.87, per 1000 atoms: 0.28
  Number of scatterers: 6681
  At special positions: 0
  Unit cell: (118.101, 99.603, 102.449, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      21     16.00
     P      47     15.00
     Mg      1     11.99
     O    1378      8.00
     N    1281      7.00
     C    3952      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 272.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 549 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 552 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 572 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 569 "
      Number of angles added : 3


  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1362

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 4 sheets defined
      61.3% alpha, 12.2% beta
      11 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 52
    Processing helix  chain 'A' and resid 53 through 85
    Processing helix  chain 'A' and resid 92 through 119
    Processing helix  chain 'A' and resid 122 through 145
    Processing helix  chain 'A' and resid 151 through 175
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.501A  pdb=" N   ASP A 212 " --> pdb=" O   MET A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 236 through 244
    Processing helix  chain 'A' and resid 341 through 345
      removed outlier: 3.575A  pdb=" N   ARG A 345 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 397
    Processing helix  chain 'A' and resid 408 through 414
    Processing helix  chain 'A' and resid 417 through 428
      removed outlier: 4.602A  pdb=" N   PHE A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 479
      removed outlier: 3.710A  pdb=" N   TRP A 442 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 445 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   ARG A 457 " --> pdb=" O   GLN A 453 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN A 478 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 518
    Processing helix  chain 'A' and resid 518 through 534
      removed outlier: 4.114A  pdb=" N   LEU A 522 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.744A  pdb=" N   SER A 564 " --> pdb=" O   ARG A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 591
    Processing helix  chain 'D' and resid 19 through 52
    Processing helix  chain 'D' and resid 53 through 64
    Processing helix  chain 'D' and resid 96 through 118
      removed outlier: 3.640A  pdb=" N   ALA D 100 " --> pdb=" O   GLN D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 121
      No H-bonds generated for 'chain 'D' and resid 119 through 121'
    Processing helix  chain 'D' and resid 122 through 145
      removed outlier: 3.519A  pdb=" N   TYR D 141 " --> pdb=" O   GLN D 137 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY D 142 " --> pdb=" O   LYS D 138 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 176
      removed outlier: 3.598A  pdb=" N   ALA D 174 " --> pdb=" O   ALA D 170 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER D 175 " --> pdb=" O   ALA D 171 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLY D 176 " --> pdb=" O   GLN D 172 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195
      removed outlier: 6.716A  pdb=" N   THR A 299 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ALA A 281 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   CYS A 297 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   LEU A 283 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LYS A 295 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   VAL A 285 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ARG A 293 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ARG A 287 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ILE A 291 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   ALA A 294 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL A  11 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLY A  10 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   ILE A 262 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ARG A 251 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   LEU A 264 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
      removed outlier: 5.643A  pdb=" N   ARG A 249 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL A 266 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   THR A 247 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323
      removed outlier: 5.947A  pdb=" N   ALA A 328 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL A 361 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323
      removed outlier: 4.142A  pdb=" N   ASP A 485 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LEU A 318 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568

    374 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      30 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1691
        1.33 -     1.45: 1571
        1.45 -     1.57: 3522
        1.57 -     1.69: 93
        1.69 -     1.81: 33
  Bond restraints: 6910
  Sorted by residual:
  bond pdb=" C   TRP A 261 "
       pdb=" N   ILE A 262 "
    ideal  model  delta    sigma   weight residual
    1.333  1.303  0.030 1.34e-02 5.57e+03 4.96e+00
  bond pdb=" C   ASP A 477 "
       pdb=" N   GLN A 478 "
    ideal  model  delta    sigma   weight residual
    1.332  1.311  0.022 1.40e-02 5.10e+03 2.40e+00
  bond pdb=" CG  LEU A 221 "
       pdb=" CD1 LEU A 221 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  bond pdb=" CB  VAL A 194 "
       pdb=" CG1 VAL A 194 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  bond pdb=" CB  PHE A 443 "
       pdb=" CG  PHE A 443 "
    ideal  model  delta    sigma   weight residual
    1.502  1.477  0.025 2.30e-02 1.89e+03 1.22e+00
  ... (remaining 6905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 9367
        1.82 -     3.64: 205
        3.64 -     5.46: 23
        5.46 -     7.28: 4
        7.28 -     9.10: 2
  Bond angle restraints: 9601
  Sorted by residual:
  angle pdb=" N   TRP A 440 "
        pdb=" CA  TRP A 440 "
        pdb=" C   TRP A 440 "
      ideal   model   delta    sigma   weight residual
     113.12  108.77    4.35 1.25e+00 6.40e-01 1.21e+01
  angle pdb=" CA  LEU A 369 "
        pdb=" CB  LEU A 369 "
        pdb=" CG  LEU A 369 "
      ideal   model   delta    sigma   weight residual
     116.30  107.20    9.10 3.50e+00 8.16e-02 6.75e+00
  angle pdb=" C   LEU A 318 "
        pdb=" N   GLY A 319 "
        pdb=" CA  GLY A 319 "
      ideal   model   delta    sigma   weight residual
     120.51  124.36   -3.85 1.63e+00 3.76e-01 5.57e+00
  angle pdb=" C   GLN A 453 "
        pdb=" N   GLU A 454 "
        pdb=" CA  GLU A 454 "
      ideal   model   delta    sigma   weight residual
     122.42  118.79    3.63 1.55e+00 4.16e-01 5.48e+00
  angle pdb=" C   ALA A 281 "
        pdb=" N   GLU A 282 "
        pdb=" CA  GLU A 282 "
      ideal   model   delta    sigma   weight residual
     122.99  119.73    3.26 1.41e+00 5.03e-01 5.34e+00
  ... (remaining 9596 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.19: 3719
       19.19 -    38.38: 318
       38.38 -    57.58: 133
       57.58 -    76.77: 68
       76.77 -    95.96: 4
  Dihedral angle restraints: 4242
    sinusoidal: 2150
      harmonic: 2092
  Sorted by residual:
  dihedral pdb=" O4'   U B   6 "
           pdb=" C1'   U B   6 "
           pdb=" N1    U B   6 "
           pdb=" C2    U B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -83.79  -76.21     1      1.50e+01 4.44e-03 3.25e+01
  dihedral pdb=" O4'   G B -11 "
           pdb=" C1'   G B -11 "
           pdb=" N9    G B -11 "
           pdb=" C4    G B -11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -171.33   65.33     1      1.70e+01 3.46e-03 1.94e+01
  dihedral pdb=" O4'   C B  15 "
           pdb=" C1'   C B  15 "
           pdb=" N1    C B  15 "
           pdb=" C2    C B  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -104.45  -55.55     1      1.50e+01 4.44e-03 1.85e+01
  ... (remaining 4239 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 688
       0.029 -    0.058: 282
       0.058 -    0.087: 86
       0.087 -    0.115: 30
       0.115 -    0.144: 10
  Chirality restraints: 1096
  Sorted by residual:
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  VAL A 268 "
            pdb=" N   VAL A 268 "
            pdb=" C   VAL A 268 "
            pdb=" CB  VAL A 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  VAL A 361 "
            pdb=" N   VAL A 361 "
            pdb=" C   VAL A 361 "
            pdb=" CB  VAL A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 1093 not shown)

  Planarity restraints: 1072
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 452 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   GLN A 452 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLN A 452 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 453 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 472 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.83e+00
        pdb=" C   ALA A 472 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ALA A 472 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 473 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 459 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.40e+00
        pdb=" C   LYS A 459 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   LYS A 459 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ALA A 460 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1069 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.38: 30
        2.38 -     3.01: 3883
        3.01 -     3.64: 10567
        3.64 -     4.27: 15151
        4.27 -     4.90: 24433
  Nonbonded interactions: 54064
  Sorted by model distance:
  nonbonded pdb=" OP1   G B -22 "
            pdb="MG    MG B 101 "
     model   vdw
     1.744 2.170
  nonbonded pdb=" OP2   C B -21 "
            pdb="MG    MG B 101 "
     model   vdw
     1.992 2.170
  nonbonded pdb=" OP1   G B  -7 "
            pdb=" NZ  LYS A  14 "
     model   vdw
     2.111 3.120
  nonbonded pdb=" OD2 ASP A 466 "
            pdb=" NE2 GLN A 470 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" O   TRP A 428 "
            pdb=" OG  SER A 436 "
     model   vdw
     2.153 3.040
  ... (remaining 54059 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.560
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
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      :  0.005   0.056   6914  Z= 0.255
  Angle     :  0.884  36.858   9604  Z= 0.391
  Chirality :  0.037   0.144   1096
  Planarity :  0.004   0.031   1072
  Dihedral  : 18.515  95.962   2880
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.70 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.32), residues: 707
  helix:  2.70 (0.25), residues: 421
  sheet: -0.24 (0.58), residues: 75
  loop : -0.43 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.019   0.002   TYR A 217 
 PHE   0.008   0.001   PHE A 443 
 TRP   0.022   0.002   TRP A 320 
 HIS   0.009   0.002   HIS A   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 6910)
  covalent geometry    : angle       0.66388 ( 9601)
  hydrogen bonds       : bond        0.17634 (  402)
  hydrogen bonds       : angle       5.92566 ( 1160)
  metal coordination   : bond        0.03504 (    4)
  metal coordination   : angle      33.04508 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6616 (mm-30)
REVERT: A  138 LYS cc_start: 0.8899 (tttt) cc_final: 0.8609 (tmtt)
REVERT: A  169 ILE cc_start: 0.8917 (mm) cc_final: 0.8404 (tp)
REVERT: A  333 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7792 (tpp80)
REVERT: A  356 SER cc_start: 0.7773 (t) cc_final: 0.7543 (p)
REVERT: A  420 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.5416 (mpp-170)
REVERT: A  530 MET cc_start: 0.8057 (mmt) cc_final: 0.7515 (mmm)
REVERT: D   27 LEU cc_start: 0.9226 (mt) cc_final: 0.8976 (mt)
REVERT: D   32 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8005 (ttp-170)
REVERT: D   42 TYR cc_start: 0.8057 (t80) cc_final: 0.7857 (t80)
REVERT: D   46 LEU cc_start: 0.9019 (mt) cc_final: 0.8653 (mt)
REVERT: D   50 TRP cc_start: 0.8448 (m100) cc_final: 0.8030 (m100)
REVERT: D   98 ARG cc_start: 0.4191 (mtt180) cc_final: 0.3519 (tpm170)
REVERT: D  115 ILE cc_start: 0.4875 (mt) cc_final: 0.4406 (mt)
REVERT: D  127 LYS cc_start: 0.9577 (tppt) cc_final: 0.9344 (tptp)
REVERT: D  163 LYS cc_start: 0.8615 (mttt) cc_final: 0.8395 (mmtt)
REVERT: D  185 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7354 (mtp180)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1508
  time to fit residues: 33.6869
Evaluate side-chains
  121 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:   40.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 419 GLN
A 449 GLN
A 516 HIS
D  30 ASN
D 143 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.170879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.134396 restraints weight = 15319.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.138634 restraints weight = 8160.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.141309 restraints weight = 5553.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.142992 restraints weight = 4361.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.143840 restraints weight = 3757.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6914  Z= 0.183
  Angle     :  0.651  11.228   9604  Z= 0.338
  Chirality :  0.039   0.164   1096
  Planarity :  0.005   0.057   1072
  Dihedral  : 18.695  98.298   1546
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.07 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.33), residues: 707
  helix:  2.74 (0.25), residues: 427
  sheet:  0.07 (0.62), residues: 73
  loop : -0.29 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 103 
 TYR   0.020   0.002   TYR A 217 
 PHE   0.008   0.001   PHE A 582 
 TRP   0.019   0.002   TRP A 450 
 HIS   0.012   0.002   HIS D 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6910)
  covalent geometry    : angle       0.64074 ( 9601)
  hydrogen bonds       : bond        0.05030 (  402)
  hydrogen bonds       : angle       4.43604 ( 1160)
  metal coordination   : bond        0.02209 (    4)
  metal coordination   : angle       6.65465 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.8092 (mtt) cc_final: 0.7819 (mtm)
REVERT: A   53 TYR cc_start: 0.7152 (m-10) cc_final: 0.6754 (m-10)
REVERT: A   93 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6385 (tp)
REVERT: A  127 LYS cc_start: 0.9265 (tmmt) cc_final: 0.9057 (tmmt)
REVERT: A  169 ILE cc_start: 0.8638 (mm) cc_final: 0.8046 (tp)
REVERT: A  356 SER cc_start: 0.7453 (t) cc_final: 0.7230 (p)
REVERT: A  420 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.5458 (mpp-170)
REVERT: D   23 GLN cc_start: 0.8840 (tp40) cc_final: 0.8567 (mt0)
REVERT: D   32 ARG cc_start: 0.8547 (ttp80) cc_final: 0.7992 (ttp-170)
REVERT: D   42 TYR cc_start: 0.8155 (t80) cc_final: 0.7809 (t80)
REVERT: D   46 LEU cc_start: 0.9181 (mt) cc_final: 0.8730 (mm)
REVERT: D   50 TRP cc_start: 0.8172 (m100) cc_final: 0.7945 (m100)
REVERT: D  138 LYS cc_start: 0.9383 (mttt) cc_final: 0.9120 (mttp)
REVERT: D  154 SER cc_start: 0.7708 (m) cc_final: 0.7506 (p)
REVERT: D  167 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8125 (mmmt)
REVERT: D  185 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7385 (mtm180)
  outliers start: 19
  outliers final: 9
  residues processed: 135
  average time/residue: 0.1125
  time to fit residues: 18.6047
Evaluate side-chains
  116 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   43 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
A 267 GLN
A 516 HIS
D  29 HIS
D 143 GLN
D 258 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.173840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.135464 restraints weight = 14491.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.139935 restraints weight = 7490.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.142866 restraints weight = 5007.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.144700 restraints weight = 3889.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.145641 restraints weight = 3324.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
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      :  0.005   0.043   6914  Z= 0.217
  Angle     :  0.650   8.015   9604  Z= 0.334
  Chirality :  0.039   0.241   1096
  Planarity :  0.005   0.048   1072
  Dihedral  : 18.656  99.151   1546
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.76 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.33), residues: 707
  helix:  2.65 (0.25), residues: 425
  sheet: -0.09 (0.62), residues: 77
  loop : -0.40 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 146 
 TYR   0.020   0.002   TYR A 217 
 PHE   0.008   0.001   PHE A 155 
 TRP   0.027   0.002   TRP A 450 
 HIS   0.011   0.002   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 6910)
  covalent geometry    : angle       0.64880 ( 9601)
  hydrogen bonds       : bond        0.04994 (  402)
  hydrogen bonds       : angle       4.44777 ( 1160)
  metal coordination   : bond        0.02148 (    4)
  metal coordination   : angle       2.55965 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.216 
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    9 MET cc_start: 0.8231 (mtt) cc_final: 0.7926 (mtm)
REVERT: A   29 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7489 (t-90)
REVERT: A   63 MET cc_start: 0.8961 (ptp) cc_final: 0.8393 (ptp)
REVERT: A  127 LYS cc_start: 0.9350 (tmmt) cc_final: 0.9065 (tmmt)
REVERT: A  185 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6904 (mtm180)
REVERT: A  356 SER cc_start: 0.7659 (t) cc_final: 0.7338 (p)
REVERT: A  475 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7311 (mm)
REVERT: A  530 MET cc_start: 0.7639 (mmp) cc_final: 0.7432 (mmp)
REVERT: D   42 TYR cc_start: 0.8183 (t80) cc_final: 0.7934 (t80)
REVERT: D   46 LEU cc_start: 0.9199 (mt) cc_final: 0.8733 (mm)
REVERT: D   50 TRP cc_start: 0.8313 (m100) cc_final: 0.8045 (m100)
REVERT: D  161 HIS cc_start: 0.8375 (m-70) cc_final: 0.8170 (m-70)
REVERT: D  167 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8214 (mmmt)
REVERT: D  185 ARG cc_start: 0.8352 (mmm160) cc_final: 0.7384 (mtm180)
  outliers start: 25
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0726
  time to fit residues: 12.6386
Evaluate side-chains
  114 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  374 ASN
Chi-restraints excluded: chain A residue  475 ILE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   43 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 74 optimal weight:   50.0000
   chunk 28 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 51 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 9 optimal weight:   30.0000
   overall best weight:    5.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
D  29 HIS
D 143 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.166317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.127630 restraints weight = 14094.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.131752 restraints weight = 7339.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.134488 restraints weight = 4928.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.136056 restraints weight = 3851.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.137228 restraints weight = 3330.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6914  Z= 0.236
  Angle     :  0.673   8.435   9604  Z= 0.347
  Chirality :  0.039   0.164   1096
  Planarity :  0.005   0.042   1072
  Dihedral  : 18.671  99.869   1546
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 21.51 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.32), residues: 707
  helix:  2.55 (0.24), residues: 425
  sheet: -0.02 (0.73), residues: 61
  loop : -0.64 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 379 
 TYR   0.018   0.002   TYR A 217 
 PHE   0.006   0.001   PHE A 155 
 TRP   0.028   0.002   TRP A 450 
 HIS   0.015   0.002   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 6910)
  covalent geometry    : angle       0.67135 ( 9601)
  hydrogen bonds       : bond        0.04944 (  402)
  hydrogen bonds       : angle       4.52798 ( 1160)
  metal coordination   : bond        0.01259 (    4)
  metal coordination   : angle       2.80373 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.144 
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    9 MET cc_start: 0.8264 (mtt) cc_final: 0.7918 (mtm)
REVERT: A   26 TRP cc_start: 0.8369 (t60) cc_final: 0.6985 (t60)
REVERT: A   29 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7460 (t-90)
REVERT: A   63 MET cc_start: 0.9107 (ptp) cc_final: 0.8506 (ptp)
REVERT: A  127 LYS cc_start: 0.9372 (tmmt) cc_final: 0.9023 (tmmt)
REVERT: A  185 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6428 (mtm-85)
REVERT: A  187 ASP cc_start: 0.8909 (p0) cc_final: 0.8666 (p0)
REVERT: A  356 SER cc_start: 0.7521 (t) cc_final: 0.7208 (p)
REVERT: A  446 ASP cc_start: 0.7955 (t0) cc_final: 0.7718 (t70)
REVERT: D   23 GLN cc_start: 0.8920 (tp40) cc_final: 0.8518 (pt0)
REVERT: D   24 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8206 (mm-40)
REVERT: D   32 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8110 (ttm-80)
REVERT: D   40 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7906 (mm)
REVERT: D   44 ASP cc_start: 0.9234 (m-30) cc_final: 0.8949 (p0)
REVERT: D   46 LEU cc_start: 0.9192 (mt) cc_final: 0.8718 (mm)
REVERT: D   50 TRP cc_start: 0.8332 (m100) cc_final: 0.7988 (m100)
REVERT: D  127 LYS cc_start: 0.9416 (tppt) cc_final: 0.8999 (tppt)
REVERT: D  167 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8281 (mmmt)
REVERT: D  184 HIS cc_start: 0.6151 (m-70) cc_final: 0.5734 (m90)
REVERT: D  185 ARG cc_start: 0.8525 (mmm160) cc_final: 0.7405 (mtm180)
  outliers start: 29
  outliers final: 20
  residues processed: 118
  average time/residue: 0.0890
  time to fit residues: 13.6068
Evaluate side-chains
  116 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  374 ASN
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain D residue   43 ASP
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  180 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   chunk 74 optimal weight:   30.0000
   chunk 2 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  29 HIS
D 143 GLN
D 260 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.164847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.127438 restraints weight = 13626.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.131455 restraints weight = 6999.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.134208 restraints weight = 4692.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.135812 restraints weight = 3642.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.136954 restraints weight = 3126.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.3935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6914  Z= 0.233
  Angle     :  0.664   8.537   9604  Z= 0.340
  Chirality :  0.039   0.162   1096
  Planarity :  0.004   0.040   1072
  Dihedral  : 18.649 100.044   1546
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 22.03 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.32), residues: 707
  helix:  2.53 (0.25), residues: 425
  sheet: -0.24 (0.73), residues: 61
  loop : -0.60 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 205 
 TYR   0.026   0.002   TYR D  42 
 PHE   0.008   0.001   PHE A 443 
 TRP   0.018   0.002   TRP A 450 
 HIS   0.013   0.002   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 6910)
  covalent geometry    : angle       0.66265 ( 9601)
  hydrogen bonds       : bond        0.04863 (  402)
  hydrogen bonds       : angle       4.48809 ( 1160)
  metal coordination   : bond        0.01185 (    4)
  metal coordination   : angle       2.60022 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.8240 (mtt) cc_final: 0.7836 (mtm)
REVERT: A   29 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7338 (t-90)
REVERT: A   63 MET cc_start: 0.8978 (ptp) cc_final: 0.8286 (ptp)
REVERT: A  119 LYS cc_start: 0.8894 (tptp) cc_final: 0.8691 (tppt)
REVERT: A  127 LYS cc_start: 0.9369 (tmmt) cc_final: 0.9000 (tmmt)
REVERT: A  138 LYS cc_start: 0.8533 (tptt) cc_final: 0.8228 (tptp)
REVERT: A  185 ARG cc_start: 0.7279 (ttp-170) cc_final: 0.6928 (mtm-85)
REVERT: D   23 GLN cc_start: 0.8874 (tp40) cc_final: 0.8524 (pt0)
REVERT: D   32 ARG cc_start: 0.8556 (ttp80) cc_final: 0.7932 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8290 (t80) cc_final: 0.7728 (t80)
REVERT: D   50 TRP cc_start: 0.8266 (m100) cc_final: 0.7930 (m100)
REVERT: D  127 LYS cc_start: 0.9398 (tppt) cc_final: 0.8938 (tppt)
REVERT: D  185 ARG cc_start: 0.8675 (mmm160) cc_final: 0.7444 (mtm180)
  outliers start: 29
  outliers final: 22
  residues processed: 114
  average time/residue: 0.1015
  time to fit residues: 14.5468
Evaluate side-chains
  114 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  374 ASN
Chi-restraints excluded: chain A residue  475 ILE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   43 ASP
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  180 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 62 optimal weight:   30.0000
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 449 GLN
D  29 HIS
D  95 GLN
D 143 GLN
D 258 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.166674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.130587 restraints weight = 13655.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.134697 restraints weight = 6994.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.137428 restraints weight = 4606.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.138974 restraints weight = 3536.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.140200 restraints weight = 3025.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6914  Z= 0.157
  Angle     :  0.599   8.374   9604  Z= 0.309
  Chirality :  0.037   0.166   1096
  Planarity :  0.004   0.039   1072
  Dihedral  : 18.522 100.586   1546
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 23.24 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.33), residues: 707
  helix:  2.61 (0.25), residues: 425
  sheet: -0.26 (0.73), residues: 61
  loop : -0.49 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 205 
 TYR   0.020   0.002   TYR D  42 
 PHE   0.006   0.001   PHE A 155 
 TRP   0.013   0.001   TRP A 152 
 HIS   0.013   0.002   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6910)
  covalent geometry    : angle       0.59754 ( 9601)
  hydrogen bonds       : bond        0.04283 (  402)
  hydrogen bonds       : angle       4.24027 ( 1160)
  metal coordination   : bond        0.00814 (    4)
  metal coordination   : angle       2.06802 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.8171 (mtt) cc_final: 0.7775 (mtm)
REVERT: A   11 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8318 (t)
REVERT: A   29 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7237 (t-90)
REVERT: A  127 LYS cc_start: 0.9355 (tmmt) cc_final: 0.9025 (tmmt)
REVERT: A  185 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.6990 (mtm180)
REVERT: A  356 SER cc_start: 0.7470 (t) cc_final: 0.7211 (p)
REVERT: A  556 ASN cc_start: 0.8570 (m-40) cc_final: 0.8075 (m110)
REVERT: D   23 GLN cc_start: 0.8866 (tp40) cc_final: 0.8508 (pt0)
REVERT: D   32 ARG cc_start: 0.8631 (ttp80) cc_final: 0.7998 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8146 (t80) cc_final: 0.7259 (t80)
REVERT: D   44 ASP cc_start: 0.9148 (m-30) cc_final: 0.8876 (p0)
REVERT: D   46 LEU cc_start: 0.9202 (mt) cc_final: 0.8784 (mt)
REVERT: D   50 TRP cc_start: 0.8133 (m100) cc_final: 0.7644 (m100)
REVERT: D  185 ARG cc_start: 0.8654 (mmm160) cc_final: 0.7443 (mtm180)
  outliers start: 32
  outliers final: 19
  residues processed: 121
  average time/residue: 0.0880
  time to fit residues: 13.7195
Evaluate side-chains
  110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  374 ASN
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain D residue   43 ASP
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  180 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0570
   chunk 70 optimal weight:    0.3980
   chunk 3 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0980
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0170
   chunk 2 optimal weight:   10.0000
   chunk 63 optimal weight:   20.0000
   overall best weight:    0.2936

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

Flipped N/Q/H residues before XYZ refinement:
** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  29 HIS
D 137 GLN
D 143 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.172911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.134044 restraints weight = 13966.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.138499 restraints weight = 7216.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.141274 restraints weight = 4815.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.143308 restraints weight = 3769.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.144266 restraints weight = 3185.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.4604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6914  Z= 0.112
  Angle     :  0.553   8.267   9604  Z= 0.288
  Chirality :  0.036   0.166   1096
  Planarity :  0.004   0.040   1072
  Dihedral  : 18.362 101.355   1546
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.65 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.32), residues: 707
  helix:  2.55 (0.24), residues: 432
  sheet: -0.10 (0.72), residues: 62
  loop : -0.46 (0.44), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  98 
 TYR   0.019   0.001   TYR D  42 
 PHE   0.008   0.001   PHE D 155 
 TRP   0.015   0.001   TRP A 152 
 HIS   0.013   0.001   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6910)
  covalent geometry    : angle       0.55235 ( 9601)
  hydrogen bonds       : bond        0.03615 (  402)
  hydrogen bonds       : angle       3.98510 ( 1160)
  metal coordination   : bond        0.00348 (    4)
  metal coordination   : angle       1.04092 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.7803 (mtt) cc_final: 0.7512 (mtm)
REVERT: A   29 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7164 (t-90)
REVERT: A  127 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9067 (tmmt)
REVERT: A  138 LYS cc_start: 0.8517 (tptt) cc_final: 0.8157 (tptp)
REVERT: A  185 ARG cc_start: 0.7411 (ttp-170) cc_final: 0.7205 (mtm180)
REVERT: A  194 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7853 (p)
REVERT: A  356 SER cc_start: 0.7316 (t) cc_final: 0.7064 (p)
REVERT: A  556 ASN cc_start: 0.8527 (m-40) cc_final: 0.8064 (m110)
REVERT: D   32 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8102 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8251 (t80) cc_final: 0.7314 (t80)
REVERT: D   46 LEU cc_start: 0.9122 (mt) cc_final: 0.8770 (mt)
REVERT: D   50 TRP cc_start: 0.8247 (m100) cc_final: 0.7885 (m100)
REVERT: D   53 TYR cc_start: 0.5904 (m-80) cc_final: 0.4876 (m-80)
REVERT: D  185 ARG cc_start: 0.8431 (mmm160) cc_final: 0.7379 (mtm180)
  outliers start: 16
  outliers final: 6
  residues processed: 118
  average time/residue: 0.0885
  time to fit residues: 13.6321
Evaluate side-chains
  101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  484 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
D  29 HIS
D 143 GLN
D 260 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.170208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.130483 restraints weight = 14010.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.134777 restraints weight = 7333.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.137635 restraints weight = 4940.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.139467 restraints weight = 3846.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.140468 restraints weight = 3282.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6914  Z= 0.152
  Angle     :  0.604  11.598   9604  Z= 0.307
  Chirality :  0.038   0.170   1096
  Planarity :  0.004   0.038   1072
  Dihedral  : 18.355 100.521   1546
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 26.51 %
    Favored  : 70.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.33), residues: 707
  helix:  2.49 (0.25), residues: 431
  sheet: -0.14 (0.72), residues: 61
  loop : -0.48 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  98 
 TYR   0.018   0.001   TYR D  42 
 PHE   0.005   0.001   PHE A 155 
 TRP   0.011   0.001   TRP A 320 
 HIS   0.013   0.002   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6910)
  covalent geometry    : angle       0.60278 ( 9601)
  hydrogen bonds       : bond        0.03953 (  402)
  hydrogen bonds       : angle       4.08783 ( 1160)
  metal coordination   : bond        0.00753 (    4)
  metal coordination   : angle       1.91951 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.7875 (mtt) cc_final: 0.7517 (mtm)
REVERT: A   29 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7224 (t-90)
REVERT: A  104 LEU cc_start: 0.9579 (tt) cc_final: 0.9247 (mt)
REVERT: A  127 LYS cc_start: 0.9413 (tmmt) cc_final: 0.9076 (tmmt)
REVERT: A  138 LYS cc_start: 0.8571 (tptt) cc_final: 0.8243 (tptp)
REVERT: A  185 ARG cc_start: 0.7441 (ttp-170) cc_final: 0.7228 (mtm180)
REVERT: A  194 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7661 (p)
REVERT: A  356 SER cc_start: 0.7508 (t) cc_final: 0.7239 (p)
REVERT: A  556 ASN cc_start: 0.8446 (m-40) cc_final: 0.8034 (m110)
REVERT: D   24 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8218 (mm-40)
REVERT: D   32 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8331 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8127 (t80) cc_final: 0.7791 (t80)
REVERT: D   46 LEU cc_start: 0.9140 (mt) cc_final: 0.8824 (mm)
REVERT: D   50 TRP cc_start: 0.8246 (m100) cc_final: 0.8021 (m100)
REVERT: D  185 ARG cc_start: 0.8475 (mmm160) cc_final: 0.7361 (mtm180)
  outliers start: 15
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0932
  time to fit residues: 11.5818
Evaluate side-chains
  100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  374 ASN
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain D residue   32 ARG
Chi-restraints excluded: chain D residue   43 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
D  29 HIS
D 143 GLN
D 260 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.168701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.128742 restraints weight = 14185.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.132957 restraints weight = 7433.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.135814 restraints weight = 5007.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.137448 restraints weight = 3902.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.138705 restraints weight = 3361.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6914  Z= 0.188
  Angle     :  0.635  11.122   9604  Z= 0.324
  Chirality :  0.039   0.169   1096
  Planarity :  0.004   0.037   1072
  Dihedral  : 18.389 100.423   1546
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 26.33 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.33), residues: 707
  helix:  2.42 (0.25), residues: 426
  sheet: -0.22 (0.71), residues: 61
  loop : -0.36 (0.44), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D 125 
 TYR   0.018   0.002   TYR D  42 
 PHE   0.006   0.001   PHE A 155 
 TRP   0.069   0.002   TRP A  50 
 HIS   0.013   0.002   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 6910)
  covalent geometry    : angle       0.63372 ( 9601)
  hydrogen bonds       : bond        0.04201 (  402)
  hydrogen bonds       : angle       4.23409 ( 1160)
  metal coordination   : bond        0.00784 (    4)
  metal coordination   : angle       2.16963 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.7856 (mtt) cc_final: 0.7455 (mtm)
REVERT: A   29 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7276 (t-90)
REVERT: A  104 LEU cc_start: 0.9554 (tt) cc_final: 0.9200 (mt)
REVERT: A  127 LYS cc_start: 0.9424 (tmmt) cc_final: 0.9080 (tmmt)
REVERT: A  138 LYS cc_start: 0.8549 (tptt) cc_final: 0.8212 (tptp)
REVERT: A  556 ASN cc_start: 0.8457 (m-40) cc_final: 0.8021 (m110)
REVERT: A  575 MET cc_start: 0.8537 (tpp) cc_final: 0.8333 (tpp)
REVERT: D   32 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8363 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8087 (t80) cc_final: 0.7778 (t80)
REVERT: D   46 LEU cc_start: 0.9149 (mt) cc_final: 0.8636 (mm)
REVERT: D  125 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8218 (ptt-90)
REVERT: D  154 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8199 (p)
REVERT: D  185 ARG cc_start: 0.8528 (mmm160) cc_final: 0.7382 (mtm180)
  outliers start: 17
  outliers final: 10
  residues processed: 96
  average time/residue: 0.0935
  time to fit residues: 11.4959
Evaluate side-chains
  100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  374 ASN
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain D residue   32 ARG
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  125 ARG
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 74 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
D  29 HIS
D 143 GLN
D 260 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.170246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.130643 restraints weight = 14158.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.134921 restraints weight = 7382.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.137810 restraints weight = 4959.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.139624 restraints weight = 3850.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.140583 restraints weight = 3298.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.4820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6914  Z= 0.142
  Angle     :  0.602   8.785   9604  Z= 0.312
  Chirality :  0.038   0.207   1096
  Planarity :  0.004   0.039   1072
  Dihedral  : 18.356 100.963   1546
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 26.85 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.33), residues: 707
  helix:  2.36 (0.25), residues: 432
  sheet: -0.21 (0.71), residues: 61
  loop : -0.50 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 125 
 TYR   0.011   0.001   TYR D  42 
 PHE   0.004   0.001   PHE A 155 
 TRP   0.021   0.002   TRP D  50 
 HIS   0.013   0.001   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6910)
  covalent geometry    : angle       0.60138 ( 9601)
  hydrogen bonds       : bond        0.03851 (  402)
  hydrogen bonds       : angle       4.17090 ( 1160)
  metal coordination   : bond        0.00454 (    4)
  metal coordination   : angle       1.70705 (    3)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.176 
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    9 MET cc_start: 0.7845 (mtt) cc_final: 0.7512 (mtm)
REVERT: A   29 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7248 (t-90)
REVERT: A  104 LEU cc_start: 0.9576 (tt) cc_final: 0.9202 (mt)
REVERT: A  127 LYS cc_start: 0.9434 (tmmt) cc_final: 0.9094 (tmmt)
REVERT: A  185 ARG cc_start: 0.6851 (mtm180) cc_final: 0.6467 (mtt180)
REVERT: A  194 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7467 (p)
REVERT: A  556 ASN cc_start: 0.8467 (m110) cc_final: 0.8030 (m110)
REVERT: A  568 ARG cc_start: 0.7730 (tpp80) cc_final: 0.6993 (tpp80)
REVERT: A  575 MET cc_start: 0.8527 (tpp) cc_final: 0.8223 (tpp)
REVERT: D   32 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8267 (ttm170)
REVERT: D   42 TYR cc_start: 0.8191 (t80) cc_final: 0.7197 (t80)
REVERT: D  154 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8478 (p)
REVERT: D  185 ARG cc_start: 0.8512 (mmm160) cc_final: 0.7352 (mtm180)
  outliers start: 17
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0784
  time to fit residues: 9.9503
Evaluate side-chains
  97 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 HIS
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  374 ASN
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain D residue   32 ARG
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
D  29 HIS
D 260 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.170073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.130293 restraints weight = 14006.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.134528 restraints weight = 7361.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.137353 restraints weight = 4955.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.139031 restraints weight = 3871.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.139992 restraints weight = 3338.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6914  Z= 0.162
  Angle     :  0.628   8.784   9604  Z= 0.322
  Chirality :  0.038   0.176   1096
  Planarity :  0.004   0.038   1072
  Dihedral  : 18.361 101.106   1546
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 27.19 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.33), residues: 707
  helix:  2.20 (0.25), residues: 432
  sheet: -0.31 (0.70), residues: 61
  loop : -0.54 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A  98 
 TYR   0.015   0.002   TYR A 141 
 PHE   0.005   0.001   PHE A 155 
 TRP   0.049   0.002   TRP D  50 
 HIS   0.013   0.002   HIS D  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6910)
  covalent geometry    : angle       0.62715 ( 9601)
  hydrogen bonds       : bond        0.03993 (  402)
  hydrogen bonds       : angle       4.25172 ( 1160)
  metal coordination   : bond        0.00505 (    4)
  metal coordination   : angle       1.75177 (    3)

===============================================================================
Job complete
usr+sys time: 1298.78 seconds
wall clock time: 23 minutes 1.27 seconds (1381.27 seconds total)