Starting phenix.real_space_refine
on Sat Aug 23 06:12:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c4o_45192/08_2025/9c4o_45192_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c4o_45192/08_2025/9c4o_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_45192/08_2025/9c4o_45192_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c4o_45192/08_2025/9c4o_45192_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c4o_45192/08_2025/9c4o_45192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c4o_45192/08_2025/9c4o_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-2.0-5787/lib/python3.9/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, 136
          Unusual residues: {' CA': 1, 'PQQ': 1}
          Classifications: {'undetermined': 2, 'water': 111}
          Link IDs: {None: 112}
  Time building chain proxies: 1.91, per 1000 atoms: 0.19
  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: 0.91
  Conformation dependent library (CDL) restraints added in 239.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.23
  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: 2.12

  Time building geometry restraints manager: 1.22 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:             2.390
  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:             0.080
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.900
  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:             0.000
  Load rotamer database and sin/cos tables:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
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 aren 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
  covalent geometry    : bond        0.00424 ( 5287)
  covalent geometry    : angle       0.64652 ( 7177)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.32478 (    2)
  hydrogen bonds       : bond        0.07766 (  280)
  hydrogen bonds       : angle       6.35315 (  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  : 0.292 
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: 1.1950
  time to fit residues: 108.0154
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  : 0.219 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3778 r_free = 0.3778 target = 0.147297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.133941 restraints weight = 11580.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 0.99
r_work: 0.3561 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.0582

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     :  0.629   6.709   7179  Z= 0.346
  Chirality :  0.044   0.184    745
  Planarity :  0.005   0.045    958
  Dihedral  :  7.039  74.777    746
  Min Nonbonded Distance : 2.169

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 aren not related in a simple way.
  whole:  0.01 (0.32), residues: 659
  helix: -1.92 (0.63), residues: 47
  sheet:  0.15 (0.25), residues: 350
  loop :  0.45 (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
  covalent geometry    : bond        0.00479 ( 5287)
  covalent geometry    : angle       0.62870 ( 7177)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.24144 (    2)
  hydrogen bonds       : bond        0.05420 (  280)
  hydrogen bonds       : angle       6.03002 (  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  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8578 (mmp) cc_final: 0.8213 (mmp)
REVERT: A  394 MET cc_start: 0.8596 (ttt) cc_final: 0.8359 (ttt)
  outliers start: 6
  outliers final: 3
  residues processed: 89
  average time/residue: 1.0512
  time to fit residues: 97.7058
Evaluate side-chains
  85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3777 r_free = 0.3777 target = 0.147179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.133804 restraints weight = 11743.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.00
r_work: 0.3559 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.0719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5288  Z= 0.260
  Angle     :  0.616   6.268   7179  Z= 0.338
  Chirality :  0.044   0.181    745
  Planarity :  0.005   0.042    958
  Dihedral  :  7.025  74.615    746
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.28 %
    Favored  : 85.61 %
  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 aren not related in a simple way.
  whole:  0.01 (0.32), residues: 659
  helix: -1.90 (0.62), residues: 47
  sheet:  0.17 (0.26), residues: 345
  loop :  0.40 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.018   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
  covalent geometry    : bond        0.00465 ( 5287)
  covalent geometry    : angle       0.61611 ( 7177)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.22785 (    2)
  hydrogen bonds       : bond        0.05337 (  280)
  hydrogen bonds       : angle       6.00544 (  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
  90 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8628 (mmp) cc_final: 0.8141 (mmp)
REVERT: A  595 ARG cc_start: 0.7734 (mtm180) cc_final: 0.7411 (ttp-170)
  outliers start: 6
  outliers final: 3
  residues processed: 87
  average time/residue: 1.2430
  time to fit residues: 112.4352
Evaluate side-chains
  85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3777 r_free = 0.3777 target = 0.147278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.133916 restraints weight = 11770.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 0.99
r_work: 0.3560 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.0778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5288  Z= 0.260
  Angle     :  0.617   6.997   7179  Z= 0.338
  Chirality :  0.044   0.183    745
  Planarity :  0.005   0.041    958
  Dihedral  :  7.067  75.505    746
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.65 %
    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 aren not related in a simple way.
  whole:  0.03 (0.32), residues: 659
  helix: -1.80 (0.62), residues: 47
  sheet:  0.18 (0.26), residues: 345
  loop :  0.41 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.017   0.002   TYR A 681 
 PHE   0.017   0.002   PHE A 352 
 TRP   0.011   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 5287)
  covalent geometry    : angle       0.61689 ( 7177)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.20018 (    2)
  hydrogen bonds       : bond        0.05299 (  280)
  hydrogen bonds       : angle       6.01994 (  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
  91 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8620 (mmp) cc_final: 0.8180 (mmp)
REVERT: A  377 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6473 (mpt)
REVERT: A  595 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7398 (ttp-170)
  outliers start: 7
  outliers final: 3
  residues processed: 88
  average time/residue: 1.2294
  time to fit residues: 112.5691
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  : 0.257 
-------------------------------------------------------------------------------
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:    0.5980
   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:    0.6980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3791 r_free = 0.3791 target = 0.148639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.135444 restraints weight = 11599.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 0.98
r_work: 0.3578 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.0897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5288  Z= 0.227
  Angle     :  0.589   6.746   7179  Z= 0.322
  Chirality :  0.044   0.173    745
  Planarity :  0.005   0.038    958
  Dihedral  :  6.944  73.644    746
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  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 aren not related in a simple way.
  whole: -0.01 (0.32), residues: 659
  helix: -1.68 (0.64), residues: 47
  sheet:  0.09 (0.26), residues: 345
  loop :  0.45 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.017   0.002   TYR A 681 
 PHE   0.016   0.002   PHE A 352 
 TRP   0.010   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5287)
  covalent geometry    : angle       0.58926 ( 7177)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       0.19207 (    2)
  hydrogen bonds       : bond        0.04899 (  280)
  hydrogen bonds       : angle       5.98228 (  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
  90 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8617 (mmp) cc_final: 0.8233 (mmp)
REVERT: A  377 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6490 (mpt)
REVERT: A  595 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7355 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8530 (mtmm) cc_final: 0.7940 (mtmp)
  outliers start: 6
  outliers final: 3
  residues processed: 87
  average time/residue: 1.3126
  time to fit residues: 118.9266
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  : 0.198 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 146 ASN
A 160 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.150196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.136997 restraints weight = 11788.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 0.99
r_work: 0.3596 rms_B_bonded: 1.17 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 2.05 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5288  Z= 0.199
  Angle     :  0.566   6.716   7179  Z= 0.308
  Chirality :  0.044   0.166    745
  Planarity :  0.004   0.037    958
  Dihedral  :  6.794  72.531    746
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.65 %
    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 aren not related in a simple way.
  whole: -0.09 (0.32), residues: 659
  helix: -1.59 (0.65), residues: 47
  sheet: -0.04 (0.25), residues: 352
  loop :  0.51 (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   0.016   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
  covalent geometry    : bond        0.00351 ( 5287)
  covalent geometry    : angle       0.56655 ( 7177)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.18417 (    2)
  hydrogen bonds       : bond        0.04523 (  280)
  hydrogen bonds       : angle       5.93018 (  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
  88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8610 (mmp) cc_final: 0.8188 (mmp)
REVERT: A  377 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6458 (mpt)
REVERT: A  595 ARG cc_start: 0.7653 (mtm180) cc_final: 0.7362 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8527 (mtmm) cc_final: 0.7934 (mtmp)
  outliers start: 6
  outliers final: 2
  residues processed: 85
  average time/residue: 1.1227
  time to fit residues: 99.4775
Evaluate side-chains
  82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3802 r_free = 0.3802 target = 0.149726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.136634 restraints weight = 11626.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 0.98
r_work: 0.3593 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3510 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1034

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= 0.209
  Angle     :  0.572   6.724   7179  Z= 0.312
  Chirality :  0.044   0.171    745
  Planarity :  0.005   0.037    958
  Dihedral  :  6.417  73.736    743
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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 aren not related in a simple way.
  whole: -0.01 (0.32), residues: 659
  helix: -1.19 (0.72), residues: 41
  sheet: -0.02 (0.26), residues: 350
  loop :  0.49 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  96 
 TYR   0.015   0.002   TYR A 681 
 PHE   0.016   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
  covalent geometry    : bond        0.00373 ( 5287)
  covalent geometry    : angle       0.57247 ( 7177)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.13179 (    2)
  hydrogen bonds       : bond        0.04656 (  280)
  hydrogen bonds       : angle       5.90717 (  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
  83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8583 (mmp) cc_final: 0.8132 (mmp)
REVERT: A  377 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6447 (mpt)
REVERT: A  595 ARG cc_start: 0.7627 (mtm180) cc_final: 0.7314 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8519 (mtmm) cc_final: 0.7917 (mtmp)
  outliers start: 4
  outliers final: 2
  residues processed: 81
  average time/residue: 1.2676
  time to fit residues: 106.9848
Evaluate side-chains
  82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3824 r_free = 0.3824 target = 0.151027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.138011 restraints weight = 11540.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 0.96
r_work: 0.3618 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 2.00 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1032

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= 0.196
  Angle     :  0.564   6.733   7179  Z= 0.307
  Chirality :  0.044   0.166    745
  Planarity :  0.005   0.036    958
  Dihedral  :  6.351  73.608    743
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 14.21 %
    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 aren not related in a simple way.
  whole: -0.13 (0.32), residues: 659
  helix: -1.60 (0.65), residues: 47
  sheet: -0.08 (0.26), residues: 352
  loop :  0.51 (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 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 5287)
  covalent geometry    : angle       0.56417 ( 7177)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.12977 (    2)
  hydrogen bonds       : bond        0.04477 (  280)
  hydrogen bonds       : angle       5.89329 (  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
  85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8647 (mmp) cc_final: 0.8193 (mmp)
REVERT: A  377 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6452 (mpt)
REVERT: A  595 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7380 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8519 (mtmm) cc_final: 0.7931 (mtmp)
  outliers start: 4
  outliers final: 2
  residues processed: 83
  average time/residue: 1.3141
  time to fit residues: 113.5575
Evaluate side-chains
  81 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3789 r_free = 0.3789 target = 0.147823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.134731 restraints weight = 11532.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 0.96
r_work: 0.3580 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3496 rms_B_bonded: 1.98 restraints_weight: 0.2500
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5288  Z= 0.263
  Angle     :  0.617   7.086   7179  Z= 0.337
  Chirality :  0.044   0.189    745
  Planarity :  0.005   0.044    958
  Dihedral  :  6.663  75.939    743
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  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 aren not related in a simple way.
  whole: -0.03 (0.32), residues: 659
  helix: -1.78 (0.63), residues: 47
  sheet:  0.09 (0.26), residues: 345
  loop :  0.44 (0.41), residues: 267

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   0.019   0.003   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 5287)
  covalent geometry    : angle       0.61679 ( 7177)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.19379 (    2)
  hydrogen bonds       : bond        0.05285 (  280)
  hydrogen bonds       : angle       5.95776 (  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
  87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8683 (mmp) cc_final: 0.8227 (mmp)
REVERT: A  377 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6509 (mpt)
REVERT: A  595 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7383 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8563 (mtmm) cc_final: 0.7980 (mtmp)
  outliers start: 6
  outliers final: 3
  residues processed: 83
  average time/residue: 1.3073
  time to fit residues: 112.6524
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  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  394 MET
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:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
A 556 GLN
A 650 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.150965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.138046 restraints weight = 11474.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 0.95
r_work: 0.3618 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 2.00 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1080

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= 0.193
  Angle     :  0.568   6.661   7179  Z= 0.308
  Chirality :  0.044   0.162    745
  Planarity :  0.005   0.039    958
  Dihedral  :  6.390  73.706    743
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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 aren not related in a simple way.
  whole: -0.12 (0.32), residues: 659
  helix: -1.61 (0.65), residues: 47
  sheet: -0.05 (0.26), residues: 350
  loop :  0.46 (0.41), residues: 262

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   0.015   0.002   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.005   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5287)
  covalent geometry    : angle       0.56779 ( 7177)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.07188 (    2)
  hydrogen bonds       : bond        0.04392 (  280)
  hydrogen bonds       : angle       5.92277 (  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
  87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8637 (mmp) cc_final: 0.8298 (mmp)
REVERT: A  377 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6488 (mpt)
REVERT: A  595 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7362 (ttp-170)
REVERT: A  645 LYS cc_start: 0.8521 (mtmm) cc_final: 0.7934 (mtmp)
  outliers start: 4
  outliers final: 2
  residues processed: 84
  average time/residue: 1.0810
  time to fit residues: 94.5939
Evaluate side-chains
  81 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 556 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 = 0.3788 r_free = 0.3788 target = 0.147828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.134760 restraints weight = 11469.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 0.95
r_work: 0.3579 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 1.97 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5288  Z= 0.265
  Angle     :  0.623   7.255   7179  Z= 0.340
  Chirality :  0.044   0.187    745
  Planarity :  0.005   0.044    958
  Dihedral  :  6.680  76.040    743
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 14.58 %
    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 aren not related in a simple way.
  whole: -0.03 (0.32), residues: 659
  helix: -1.78 (0.63), residues: 47
  sheet:  0.09 (0.26), residues: 345
  loop :  0.44 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 287 
 TYR   0.016   0.002   TYR A 681 
 PHE   0.019   0.003   PHE A 352 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 5287)
  covalent geometry    : angle       0.62287 ( 7177)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.14924 (    2)
  hydrogen bonds       : bond        0.05277 (  280)
  hydrogen bonds       : angle       5.94282 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4093.40 seconds
wall clock time: 70 minutes 1.84 seconds (4201.84 seconds total)