Starting phenix.real_space_refine
on Thu Jul  2 20:39:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c4o_45192/07_2026/9c4o_45192_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c4o_45192/07_2026/9c4o_45192.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c4o_45192/07_2026/9c4o_45192_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c4o_45192/07_2026/9c4o_45192_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c4o_45192/07_2026/9c4o_45192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c4o_45192/07_2026/9c4o_45192.map"
  }
  resolution = 1.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.064
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      19      5.16       5
     C    3205      2.51       5
     N     915      2.21       5
     O    1143      1.98       5
     H    4883      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10166
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 661, 10030
          Classifications: {'peptide': 661}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 633}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 135
          Ad-hoc single atom residues: {' CA': 1}
          Unusual residues: {'PQQ': 1}
          Classifications: {'undetermined': 1, 'water': 111}
          Link IDs: {None: 111}
          Chain breaks: 1
  Time building chain proxies: 1.69, per 1000 atoms: 0.17
  Number of scatterers: 10166
  At special positions: 0
  Unit cell: (86.92, 62.32, 72.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      19     16.00
     O    1143      8.00
     N     915      7.00
     C    3205      6.00
     H    4883      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 585 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 199.3 milliseconds
  

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1178

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 6 sheets defined
      6.5% alpha, 53.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 64 through 69
      removed outlier: 3.987A  pdb=" N   THR A  69 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 253 through 260
    Processing helix  chain 'A' and resid 264 through 271
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.861A  pdb=" N   GLN A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 481
      removed outlier: 4.264A  pdb=" N   TYR A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51
      removed outlier: 4.284A  pdb=" N   ALA A  46 " --> pdb=" O   ARG A 137 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ASN A 132 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ARG A 105 " --> pdb=" O   MET A 152 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   VAL A 154 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   TYR A 107 " --> pdb=" O   VAL A 154 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   THR A 156 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77
    Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 172
      removed outlier: 4.451A  pdb=" N   TRP A 405 " --> pdb=" O   PRO A 349 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   THR A 351 " --> pdb=" O   THR A 403 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   THR A 403 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   THR A 353 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   LEU A 401 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   GLY A 355 " --> pdb=" O   PRO A 399 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ASN A 357 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ILE A 397 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU A 359 " --> pdb=" O   TRP A 395 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   TRP A 395 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   MET A 361 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   LEU A 393 " --> pdb=" O   MET A 361 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   GLU A 363 " --> pdb=" O   ARG A 391 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ARG A 391 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ARG A 365 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASP A 389 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   GLY A 367 " --> pdb=" O   ARG A 387 " (cutoff:3.500A)
      removed outlier: 9.712A  pdb=" N   TRP A 447 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   PHE A 471 " --> pdb=" O   TRP A 447 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   LEU A 513 " --> pdb=" O   GLN A 556 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   GLN A 556 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   SER A 515 " --> pdb=" O   TRP A 554 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   TRP A 554 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ALA A 517 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   LEU A 552 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   PHE A 519 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   ALA A 550 " --> pdb=" O   PHE A 519 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   THR A 521 " --> pdb=" O   GLN A 548 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   GLN A 548 " --> pdb=" O   THR A 521 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR A 523 " --> pdb=" O   ARG A 546 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ARG A 546 " --> pdb=" O   THR A 523 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ASP A 525 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   LYS A 544 " --> pdb=" O   ASP A 525 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   ILE A 527 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ALA A 542 " --> pdb=" O   ILE A 527 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   VAL A 529 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   LYS A 540 " --> pdb=" O   VAL A 529 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 562 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373
    Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 623
    Processing sheet with id=AA6, first strand: chain 'A' and resid 668 through 671
      removed outlier: 3.561A  pdb=" N   SER A 670 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.08

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4883
        1.03 -     1.23: 15
        1.23 -     1.42: 2322
        1.42 -     1.62: 2914
        1.62 -     1.81: 36
  Bond restraints: 10170
  Sorted by residual:
  bond pdb=" C   PRO A 683 "
       pdb=" N   SER A 684 "
    ideal  model  delta    sigma   weight residual
    1.327  1.308  0.018 1.71e-02 3.42e+03 1.16e+00
  bond pdb=" CA  LYS A 277 "
       pdb=" C   LYS A 277 "
    ideal  model  delta    sigma   weight residual
    1.526  1.515  0.011 1.08e-02 8.57e+03 1.03e+00
  bond pdb=" C   ALA A 450 "
       pdb=" N   GLY A 451 "
    ideal  model  delta    sigma   weight residual
    1.330  1.317  0.013 1.32e-02 5.74e+03 9.14e-01
  bond pdb=" C   GLU A 363 "
       pdb=" N   ASN A 364 "
    ideal  model  delta    sigma   weight residual
    1.331  1.318  0.013 1.40e-02 5.10e+03 8.48e-01
  bond pdb=" C   ARG A 589 "
       pdb=" N   MET A 590 "
    ideal  model  delta    sigma   weight residual
    1.326  1.309  0.017 1.84e-02 2.95e+03 8.42e-01
  ... (remaining 10165 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 17527
        1.29 -     2.58: 613
        2.58 -     3.88: 50
        3.88 -     5.17: 12
        5.17 -     6.46: 2
  Bond angle restraints: 18204
  Sorted by residual:
  angle pdb=" N   GLY A 492 "
        pdb=" CA  GLY A 492 "
        pdb=" C   GLY A 492 "
      ideal   model   delta    sigma   weight residual
     114.67  111.15    3.52 1.10e+00 8.26e-01 1.02e+01
  angle pdb=" N   ASP A 530 "
        pdb=" CA  ASP A 530 "
        pdb=" C   ASP A 530 "
      ideal   model   delta    sigma   weight residual
     111.24  108.22    3.02 1.29e+00 6.01e-01 5.48e+00
  angle pdb=" N   SER A 375 "
        pdb=" CA  SER A 375 "
        pdb=" C   SER A 375 "
      ideal   model   delta    sigma   weight residual
     112.12  108.99    3.13 1.34e+00 5.57e-01 5.46e+00
  angle pdb=" N   PRO A 685 "
        pdb=" CA  PRO A 685 "
        pdb=" C   PRO A 685 "
      ideal   model   delta    sigma   weight residual
     112.47  116.85   -4.38 2.06e+00 2.36e-01 4.52e+00
  angle pdb=" CA  VAL A 348 "
        pdb=" C   VAL A 348 "
        pdb=" N   PRO A 349 "
      ideal   model   delta    sigma   weight residual
     117.33  119.30   -1.97 1.01e+00 9.80e-01 3.82e+00
  ... (remaining 18199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 4301
       17.76 -    35.52: 360
       35.52 -    53.28: 114
       53.28 -    71.04: 37
       71.04 -    88.80: 16
  Dihedral angle restraints: 4828
    sinusoidal: 2618
      harmonic: 2210
  Sorted by residual:
  dihedral pdb=" CA  TYR A 680 "
           pdb=" C   TYR A 680 "
           pdb=" N   TYR A 681 "
           pdb=" CA  TYR A 681 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.89  -25.11     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  PRO A 685 "
           pdb=" C   PRO A 685 "
           pdb=" N   GLY A 686 "
           pdb=" CA  GLY A 686 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.22  -24.78     0      5.00e+00 4.00e-02 2.46e+01
  dihedral pdb=" CA  ASP A 398 "
           pdb=" C   ASP A 398 "
           pdb=" N   PRO A 399 "
           pdb=" CA  PRO A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.87   24.13     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 4825 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 454
       0.034 -    0.068: 216
       0.068 -    0.102: 45
       0.102 -    0.137: 29
       0.137 -    0.171: 1
  Chirality restraints: 745
  Sorted by residual:
  chirality pdb=" CA  PRO A 685 "
            pdb=" N   PRO A 685 "
            pdb=" C   PRO A 685 "
            pdb=" CB  PRO A 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.29e-01
  chirality pdb=" CA  ILE A 501 "
            pdb=" N   ILE A 501 "
            pdb=" C   ILE A 501 "
            pdb=" CB  ILE A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  ILE A 104 "
            pdb=" N   ILE A 104 "
            pdb=" C   ILE A 104 "
            pdb=" CB  ILE A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 742 not shown)

  Planarity restraints: 1591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 684 "    0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO A 685 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 685 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 685 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  91 "    0.114 9.50e-02 1.11e+02   3.82e-02 1.62e+00
        pdb=" NE  ARG A  91 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  91 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  91 "    0.004 2.00e-02 2.50e+03
        pdb="HH11 ARG A  91 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG A  91 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A  91 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A  91 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 192 "   -0.021 5.00e-02 4.00e+02   3.12e-02 1.56e+00
        pdb=" N   PRO A 193 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1588 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 714
        2.18 -     2.79: 21047
        2.79 -     3.39: 30425
        3.39 -     4.00: 43620
        4.00 -     4.60: 63096
  Nonbonded interactions: 158902
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 479 "
            pdb=" H   ASN A 490 "
     model   vdw
     1.575 2.450
  nonbonded pdb=" HH  TYR A 481 "
            pdb=" O2B PQQ A 802 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" HH  TYR A 464 "
            pdb=" OE2 GLU A 502 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" O   VAL A 638 "
            pdb=" H   LEU A 662 "
     model   vdw
     1.616 2.450
  nonbonded pdb="HD21 ASN A 357 "
            pdb=" OE2 GLU A 359 "
     model   vdw
     1.627 2.450
  ... (remaining 158897 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.040
  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:             0.070
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.610
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5288  Z= 0.249
  Angle     :  0.646   6.461   7179  Z= 0.367
  Chirality :  0.044   0.171    745
  Planarity :  0.005   0.051    958
  Dihedral  : 16.532  88.799   1925
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 14.76 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.32), residues: 659
  helix: -1.84 (0.64), residues: 47
  sheet:  0.18 (0.25), residues: 349
  loop :  0.34 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 287 
 TYR   0.017   0.002   TYR A 681 
 PHE   0.016   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 445 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.25 ( 5287)
  covalent geometry    : angle       0.64652 /  0.37 ( 7177)
  SS BOND              : bond        0.00037 /  0.02 (    1)
  SS BOND              : angle       0.32478 /  0.17 (    2)
  hydrogen bonds       : bond        0.07766 /  5.26 (  280)
  hydrogen bonds       : angle       6.35315 /  4.57 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8545 (mmp) cc_final: 0.8331 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 87
  average time/residue: 1.1146
  time to fit residues: 101.0742
Evaluate side-chains
  84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.147402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.134054 restraints weight = 11580.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 0.99
r_work: 0.3562 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.0589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5288  Z= 0.268
  Angle     :  0.628   6.726   7179  Z= 0.345
  Chirality :  0.044   0.185    745
  Planarity :  0.005   0.044    958
  Dihedral  :  7.036  74.793    746
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.92 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.32), residues: 659
  helix: -1.91 (0.63), residues: 47
  sheet:  0.16 (0.25), residues: 350
  loop :  0.43 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 387 
 TYR   0.019   0.002   TYR A 681 
 PHE   0.018   0.003   PHE A 352 
 TRP   0.011   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 342 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00480 /  0.27 ( 5287)
  covalent geometry    : angle       0.62823 /  0.35 ( 7177)
  SS BOND              : bond        0.00069 /  0.04 (    1)
  SS BOND              : angle       0.24371 /  0.13 (    2)
  hydrogen bonds       : bond        0.05424 /  3.69 (  280)
  hydrogen bonds       : angle       6.03357 /  4.34 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  91 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8572 (mmp) cc_final: 0.8205 (mmp)
REVERT: A  394 MET cc_start: 0.8598 (ttt) cc_final: 0.8360 (ttt)
  outliers start: 6
  outliers final: 3
  residues processed: 89
  average time/residue: 1.0105
  time to fit residues: 93.7861
Evaluate side-chains
  84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0030
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 146 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.149936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.136786 restraints weight = 11768.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 0.98
r_work: 0.3595 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.0759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5288  Z= 0.210
  Angle     :  0.576   6.009   7179  Z= 0.315
  Chirality :  0.044   0.167    745
  Planarity :  0.004   0.039    958
  Dihedral  :  6.797  73.476    746
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 14.02 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.32), residues: 659
  helix: -1.78 (0.64), residues: 47
  sheet:  0.03 (0.25), residues: 350
  loop :  0.42 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.017   0.001   TYR A 681 
 PHE   0.016   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.21 ( 5287)
  covalent geometry    : angle       0.57568 /  0.31 ( 7177)
  SS BOND              : bond        0.00004 /  0.00 (    1)
  SS BOND              : angle       0.23082 /  0.12 (    2)
  hydrogen bonds       : bond        0.04683 /  3.18 (  280)
  hydrogen bonds       : angle       5.95595 /  4.30 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8589 (mmp) cc_final: 0.8146 (mmp)
REVERT: A  364 ASN cc_start: 0.7789 (m110) cc_final: 0.7522 (t0)
REVERT: A  394 MET cc_start: 0.8523 (ttt) cc_final: 0.8278 (ttt)
REVERT: A  595 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7359 (ttp-170)
  outliers start: 3
  outliers final: 3
  residues processed: 87
  average time/residue: 1.2021
  time to fit residues: 108.9064
Evaluate side-chains
  83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 64 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 ASN
A 650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.150931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.137761 restraints weight = 11753.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 0.98
r_work: 0.3605 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5288  Z= 0.195
  Angle     :  0.564   6.471   7179  Z= 0.307
  Chirality :  0.044   0.166    745
  Planarity :  0.004   0.037    958
  Dihedral  :  6.734  73.749    746
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.02 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.32), residues: 659
  helix: -1.19 (0.72), residues: 41
  sheet: -0.04 (0.25), residues: 350
  loop :  0.53 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  96 
 TYR   0.016   0.001   TYR A 681 
 PHE   0.016   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.20 ( 5287)
  covalent geometry    : angle       0.56373 /  0.31 ( 7177)
  SS BOND              : bond        0.00008 /  0.00 (    1)
  SS BOND              : angle       0.18411 /  0.10 (    2)
  hydrogen bonds       : bond        0.04470 /  3.05 (  280)
  hydrogen bonds       : angle       5.91224 /  4.27 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  90 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8558 (mmp) cc_final: 0.8127 (mmp)
REVERT: A  364 ASN cc_start: 0.7702 (m110) cc_final: 0.7453 (t0)
REVERT: A  377 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6452 (mpt)
REVERT: A  394 MET cc_start: 0.8506 (ttt) cc_final: 0.8246 (ttt)
REVERT: A  595 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7366 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8486 (mtmm) cc_final: 0.7894 (mtmp)
  outliers start: 6
  outliers final: 3
  residues processed: 88
  average time/residue: 1.0166
  time to fit residues: 93.7568
Evaluate side-chains
  83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 ASN
A 650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.148961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.135726 restraints weight = 11603.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 0.98
r_work: 0.3582 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.0878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5288  Z= 0.235
  Angle     :  0.591   6.847   7179  Z= 0.323
  Chirality :  0.044   0.178    745
  Planarity :  0.005   0.038    958
  Dihedral  :  6.921  75.192    746
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.84 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.32), residues: 659
  helix: -1.67 (0.64), residues: 47
  sheet:  0.05 (0.26), residues: 345
  loop :  0.47 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.016   0.002   TYR A 681 
 PHE   0.017   0.002   PHE A 352 
 TRP   0.010   0.001   TRP A 568 
 HIS   0.001   0.001   HIS A 445 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.23 ( 5287)
  covalent geometry    : angle       0.59122 /  0.32 ( 7177)
  SS BOND              : bond        0.00045 /  0.02 (    1)
  SS BOND              : angle       0.18101 /  0.10 (    2)
  hydrogen bonds       : bond        0.04986 /  3.40 (  280)
  hydrogen bonds       : angle       5.91573 /  4.28 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  91 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8601 (mmp) cc_final: 0.8233 (mmp)
REVERT: A  364 ASN cc_start: 0.7746 (m110) cc_final: 0.7505 (t0)
REVERT: A  377 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6482 (mpt)
REVERT: A  595 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7339 (ttp-170)
  outliers start: 6
  outliers final: 3
  residues processed: 88
  average time/residue: 1.1013
  time to fit residues: 101.4397
Evaluate side-chains
  84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0370
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.4980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 146 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 ASN
A 650 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.151950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.138856 restraints weight = 11799.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 0.98
r_work: 0.3618 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5288  Z= 0.180
  Angle     :  0.550   6.514   7179  Z= 0.299
  Chirality :  0.044   0.161    745
  Planarity :  0.004   0.035    958
  Dihedral  :  6.691  73.121    746
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.21 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.32), residues: 659
  helix: -1.54 (0.66), residues: 47
  sheet: -0.11 (0.25), residues: 352
  loop :  0.54 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.015   0.001   TYR A 681 
 PHE   0.015   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 649 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.18 ( 5287)
  covalent geometry    : angle       0.55038 /  0.30 ( 7177)
  SS BOND              : bond        0.00002 /  0.00 (    1)
  SS BOND              : angle       0.12680 /  0.07 (    2)
  hydrogen bonds       : bond        0.04218 /  2.88 (  280)
  hydrogen bonds       : angle       5.89515 /  4.27 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  89 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8582 (mmp) cc_final: 0.8168 (mmp)
REVERT: A  377 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6445 (mpt)
REVERT: A  379 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6734 (tm-30)
REVERT: A  595 ARG cc_start: 0.7635 (mtm180) cc_final: 0.7335 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8511 (mtmm) cc_final: 0.7917 (mtmp)
  outliers start: 5
  outliers final: 2
  residues processed: 87
  average time/residue: 1.0989
  time to fit residues: 100.2264
Evaluate side-chains
  87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.2980
   chunk 57 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 160 GLN
A 578 ASN
A 650 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.151278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138208 restraints weight = 11636.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 0.97
r_work: 0.3611 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5288  Z= 0.194
  Angle     :  0.560   6.760   7179  Z= 0.305
  Chirality :  0.044   0.165    745
  Planarity :  0.004   0.038    958
  Dihedral  :  6.724  73.511    746
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.39 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.32), residues: 659
  helix: -1.56 (0.65), residues: 47
  sheet: -0.08 (0.26), residues: 352
  loop :  0.56 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 287 
 TYR   0.015   0.001   TYR A 681 
 PHE   0.016   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.19 ( 5287)
  covalent geometry    : angle       0.56054 /  0.30 ( 7177)
  SS BOND              : bond        0.00009 /  0.00 (    1)
  SS BOND              : angle       0.17216 /  0.09 (    2)
  hydrogen bonds       : bond        0.04430 /  3.02 (  280)
  hydrogen bonds       : angle       5.86937 /  4.25 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  90 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8587 (mmp) cc_final: 0.8139 (mmp)
REVERT: A  377 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6453 (mpt)
REVERT: A  595 ARG cc_start: 0.7644 (mtm180) cc_final: 0.7341 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8506 (mtmm) cc_final: 0.7913 (mtmp)
  outliers start: 6
  outliers final: 3
  residues processed: 86
  average time/residue: 1.1894
  time to fit residues: 106.8996
Evaluate side-chains
  86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0970
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.9780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 578 ASN
A 650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.150301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.137172 restraints weight = 11507.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 0.96
r_work: 0.3608 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 1.99 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5288  Z= 0.221
  Angle     :  0.582   7.050   7179  Z= 0.317
  Chirality :  0.044   0.174    745
  Planarity :  0.005   0.037    958
  Dihedral  :  6.847  74.297    746
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.21 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.32), residues: 659
  helix: -1.67 (0.64), residues: 47
  sheet: -0.03 (0.26), residues: 352
  loop :  0.53 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 287 
 TYR   0.015   0.002   TYR A 681 
 PHE   0.017   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 649 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.22 ( 5287)
  covalent geometry    : angle       0.58177 /  0.32 ( 7177)
  SS BOND              : bond        0.00032 /  0.02 (    1)
  SS BOND              : angle       0.15917 /  0.09 (    2)
  hydrogen bonds       : bond        0.04757 /  3.25 (  280)
  hydrogen bonds       : angle       5.88909 /  4.26 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8656 (mmp) cc_final: 0.8206 (mmp)
REVERT: A  377 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6490 (mpt)
REVERT: A  595 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7387 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8529 (mtmm) cc_final: 0.7946 (mtmp)
  outliers start: 5
  outliers final: 3
  residues processed: 85
  average time/residue: 1.2761
  time to fit residues: 113.1887
Evaluate side-chains
  85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 44 optimal weight:    0.1980
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 160 GLN
A 578 ASN
A 650 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.152998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.140037 restraints weight = 11550.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 0.96
r_work: 0.3641 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5288  Z= 0.171
  Angle     :  0.547   6.677   7179  Z= 0.296
  Chirality :  0.044   0.156    745
  Planarity :  0.004   0.037    958
  Dihedral  :  6.610  72.144    746
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.02 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.33), residues: 659
  helix: -1.50 (0.67), residues: 47
  sheet: -0.12 (0.26), residues: 352
  loop :  0.58 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 287 
 TYR   0.014   0.001   TYR A 681 
 PHE   0.014   0.002   PHE A 352 
 TRP   0.008   0.001   TRP A 568 
 HIS   0.003   0.001   HIS A 649 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.17 ( 5287)
  covalent geometry    : angle       0.54720 /  0.30 ( 7177)
  SS BOND              : bond        0.00007 /  0.00 (    1)
  SS BOND              : angle       0.14662 /  0.08 (    2)
  hydrogen bonds       : bond        0.04092 /  2.80 (  280)
  hydrogen bonds       : angle       5.85798 /  4.24 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  89 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8616 (mmp) cc_final: 0.8150 (mmp)
REVERT: A  377 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6445 (mpt)
REVERT: A  565 ASN cc_start: 0.7892 (m-40) cc_final: 0.7638 (t0)
REVERT: A  595 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7352 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8501 (mtmm) cc_final: 0.7917 (mtmp)
  outliers start: 5
  outliers final: 3
  residues processed: 86
  average time/residue: 1.2134
  time to fit residues: 109.2564
Evaluate side-chains
  85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 650 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.150774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.137761 restraints weight = 11440.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 0.95
r_work: 0.3615 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 1.99 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5288  Z= 0.213
  Angle     :  0.580   6.961   7179  Z= 0.315
  Chirality :  0.044   0.173    745
  Planarity :  0.005   0.037    958
  Dihedral  :  6.788  73.453    746
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 14.02 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.33), residues: 659
  helix: -1.61 (0.65), residues: 47
  sheet: -0.04 (0.26), residues: 352
  loop :  0.55 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 287 
 TYR   0.015   0.002   TYR A 681 
 PHE   0.017   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.003   0.001   HIS A 649 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.21 ( 5287)
  covalent geometry    : angle       0.57974 /  0.31 ( 7177)
  SS BOND              : bond        0.00014 /  0.01 (    1)
  SS BOND              : angle       0.13810 /  0.07 (    2)
  hydrogen bonds       : bond        0.04643 /  3.18 (  280)
  hydrogen bonds       : angle       5.87070 /  4.26 (  795)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  515 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8645 (mmp) cc_final: 0.8179 (mmp)
REVERT: A  377 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6472 (mpt)
REVERT: A  595 ARG cc_start: 0.7647 (mtm180) cc_final: 0.7365 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8517 (mtmm) cc_final: 0.7930 (mtmp)
  outliers start: 4
  outliers final: 3
  residues processed: 82
  average time/residue: 1.2406
  time to fit residues: 106.4068
Evaluate side-chains
  84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  404 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 160 GLN
A 650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.151832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.138856 restraints weight = 11477.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 0.95
r_work: 0.3629 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 1.99 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5288  Z= 0.192
  Angle     :  0.564   6.834   7179  Z= 0.305
  Chirality :  0.044   0.162    745
  Planarity :  0.005   0.036    958
  Dihedral  :  6.692  72.510    746
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.84 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.33), residues: 659
  helix: -1.55 (0.66), residues: 47
  sheet: -0.08 (0.26), residues: 352
  loop :  0.59 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 287 
 TYR   0.014   0.001   TYR A 681 
 PHE   0.016   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A 649 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.19 ( 5287)
  covalent geometry    : angle       0.56436 /  0.31 ( 7177)
  SS BOND              : bond        0.00008 /  0.00 (    1)
  SS BOND              : angle       0.14113 /  0.07 (    2)
  hydrogen bonds       : bond        0.04361 /  2.98 (  280)
  hydrogen bonds       : angle       5.86840 /  4.25 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4291.75 seconds
wall clock time: 73 minutes 30.86 seconds (4410.86 seconds total)