Starting phenix.real_space_refine
on Fri Aug 22 19:23:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b0n_15789/08_2025/8b0n_15789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b0n_15789/08_2025/8b0n_15789.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b0n_15789/08_2025/8b0n_15789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b0n_15789/08_2025/8b0n_15789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b0n_15789/08_2025/8b0n_15789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b0n_15789/08_2025/8b0n_15789.cif"
  }
  resolution = 2.67
  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=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3852 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      15      5.16       5
     C    2635      2.51       5
     N     660      2.21       5
     O     693      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 4004
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 510, 3972
          Classifications: {'peptide': 510}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 36, 'TRANS': 473}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'P1L:plan-1': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'OU9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.30, per 1000 atoms: 0.32
  Number of scatterers: 4004
  At special positions: 0
  Unit cell: (59.472, 82.6, 85.904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P       1     15.00
     O     693      8.00
     N     660      7.00
     C    2635      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 155.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      57.5% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 9 through 24
      removed outlier: 3.560A  pdb=" N   GLY A  24 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 28
    Processing helix  chain 'A' and resid 34 through 47
      removed outlier: 3.934A  pdb=" N   ILE A  38 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 74 through 81
      removed outlier: 3.653A  pdb=" N   SER A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 116
      removed outlier: 4.257A  pdb=" N   TYR A 104 " --> pdb=" O   TYR A 100 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   THR A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 126
    Processing helix  chain 'A' and resid 126 through 140
      removed outlier: 3.606A  pdb=" N   ALA A 130 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 145
      removed outlier: 3.724A  pdb=" N   THR A 144 " --> pdb=" O   TRP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 157
      removed outlier: 4.571A  pdb=" N   ASP A 157 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 162
      No H-bonds generated for 'chain 'A' and resid 160 through 162'
    Processing helix  chain 'A' and resid 163 through 168
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 3.645A  pdb=" N   ILE A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 204
      removed outlier: 4.053A  pdb=" N   LEU A 195 " --> pdb=" O   ASN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 211
    Processing helix  chain 'A' and resid 218 through 221
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 4.520A  pdb=" N   TRP A 237 " --> pdb=" O   GLN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 254
      removed outlier: 4.389A  pdb=" N   LEU A 243 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASN A 244 " --> pdb=" O   GLY A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 3.569A  pdb=" N   LYS A 291 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 349
      removed outlier: 4.318A  pdb=" N   SER A 349 " --> pdb=" O   PRO A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 400
    Processing helix  chain 'A' and resid 419 through 437
      removed outlier: 4.399A  pdb=" N   TRP A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG A 432 " --> pdb=" O   MET A 428 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA A 433 " --> pdb=" O   ALA A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 486
    Processing helix  chain 'A' and resid 488 through 509
    Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216
    Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273
      removed outlier: 3.823A  pdb=" N   VAL A 300 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ASP A 272 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ALA A 302 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273
      removed outlier: 3.823A  pdb=" N   VAL A 300 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ASP A 272 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ALA A 302 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ILE A 263 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   GLY A 298 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   GLN A 223 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   ILE A 264 " --> pdb=" O   GLN A 223 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   SER A 225 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 376
      removed outlier: 6.443A  pdb=" N   GLU A 381 " --> pdb=" O   TYR A 406 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A 408 " --> pdb=" O   GLU A 381 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   THR A 383 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   ILE A 410 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ALA A 385 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   SER A 443 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR A 409 " --> pdb=" O   SER A 443 " (cutoff:3.500A)

    211 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 612
        1.31 -     1.43: 1141
        1.43 -     1.56: 2333
        1.56 -     1.68: 1
        1.68 -     1.80: 29
  Bond restraints: 4116
  Sorted by residual:
  bond pdb=" N   P1L A 387 "
       pdb=" CA  P1L A 387 "
    ideal  model  delta    sigma   weight residual
    1.442  1.489 -0.047 2.00e-02 2.50e+03 5.61e+00
  bond pdb=" C   P1L A 387 "
       pdb=" O   P1L A 387 "
    ideal  model  delta    sigma   weight residual
    1.234  1.188  0.046 2.00e-02 2.50e+03 5.35e+00
  bond pdb=" O11 OU9 A 601 "
       pdb=" P   OU9 A 601 "
    ideal  model  delta    sigma   weight residual
    1.650  1.695 -0.045 2.00e-02 2.50e+03 5.10e+00
  bond pdb=" C11 OU9 A 601 "
       pdb=" O13 OU9 A 601 "
    ideal  model  delta    sigma   weight residual
    1.418  1.375  0.043 2.00e-02 2.50e+03 4.66e+00
  bond pdb=" SG  P1L A 387 "
       pdb=" C7  P1L A 387 "
    ideal  model  delta    sigma   weight residual
    1.733  1.691  0.042 2.00e-02 2.50e+03 4.40e+00
  ... (remaining 4111 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 5517
        1.77 -     3.54: 75
        3.54 -     5.30: 18
        5.30 -     7.07: 5
        7.07 -     8.84: 2
  Bond angle restraints: 5617
  Sorted by residual:
  angle pdb=" SG  P1L A 387 "
        pdb=" C7  P1L A 387 "
        pdb=" C8  P1L A 387 "
      ideal   model   delta    sigma   weight residual
     109.23  118.07   -8.84 3.00e+00 1.11e-01 8.68e+00
  angle pdb=" CA  P1L A 387 "
        pdb=" C   P1L A 387 "
        pdb=" O   P1L A 387 "
      ideal   model   delta    sigma   weight residual
     128.33  121.11    7.22 3.00e+00 1.11e-01 5.79e+00
  angle pdb=" N   GLY A  43 "
        pdb=" CA  GLY A  43 "
        pdb=" C   GLY A  43 "
      ideal   model   delta    sigma   weight residual
     114.66  111.80    2.86 1.24e+00 6.50e-01 5.32e+00
  angle pdb=" SG  P1L A 387 "
        pdb=" C7  P1L A 387 "
        pdb=" O7  P1L A 387 "
      ideal   model   delta    sigma   weight residual
     126.61  120.10    6.51 3.00e+00 1.11e-01 4.71e+00
  angle pdb=" C2  OU9 A 601 "
        pdb=" C1  OU9 A 601 "
        pdb=" O11 OU9 A 601 "
      ideal   model   delta    sigma   weight residual
     113.71  107.45    6.26 3.00e+00 1.11e-01 4.36e+00
  ... (remaining 5612 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 2284
       15.57 -    31.14: 112
       31.14 -    46.71: 17
       46.71 -    62.28: 9
       62.28 -    77.85: 4
  Dihedral angle restraints: 2426
    sinusoidal: 960
      harmonic: 1466
  Sorted by residual:
  dihedral pdb=" CA  PHE A  28 "
           pdb=" C   PHE A  28 "
           pdb=" N   SER A  29 "
           pdb=" CA  SER A  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.02  -20.98     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CB  GLU A 435 "
           pdb=" CG  GLU A 435 "
           pdb=" CD  GLU A 435 "
           pdb=" OE1 GLU A 435 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   77.85  -77.85     1      3.00e+01 1.11e-03 8.42e+00
  dihedral pdb=" CA  TYR A 406 "
           pdb=" C   TYR A 406 "
           pdb=" N   LEU A 407 "
           pdb=" CA  LEU A 407 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.13   13.87     0      5.00e+00 4.00e-02 7.69e+00
  ... (remaining 2423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 483
       0.045 -    0.089: 101
       0.089 -    0.134: 44
       0.134 -    0.178: 2
       0.178 -    0.223: 2
  Chirality restraints: 632
  Sorted by residual:
  chirality pdb=" CA  P1L A 387 "
            pdb=" N   P1L A 387 "
            pdb=" C   P1L A 387 "
            pdb=" CB  P1L A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.27    2.49   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" C2  OU9 A 601 "
            pdb=" C1  OU9 A 601 "
            pdb=" C3  OU9 A 601 "
            pdb=" O21 OU9 A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.73   -0.18 2.00e-01 2.50e+01 8.44e-01
  chirality pdb=" CA  TRP A 489 "
            pdb=" N   TRP A 489 "
            pdb=" C   TRP A 489 "
            pdb=" CB  TRP A 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 629 not shown)

  Planarity restraints: 705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  87 "    0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO A  88 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  34 "   -0.022 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A  35 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A  35 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  35 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 204 "   -0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO A 205 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 205 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 205 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 702 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 964
        2.79 -     3.32: 3989
        3.32 -     3.85: 6977
        3.85 -     4.37: 8714
        4.37 -     4.90: 14571
  Nonbonded interactions: 35215
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 333 "
            pdb=" OE1 GLU A 389 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   PHE A 151 "
            pdb=" OG  SER A 154 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER A 225 "
            pdb=" OG  SER A 260 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   GLY A 229 "
            pdb=" NH1 ARG A 467 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   PRO A 361 "
            pdb=" N   OU9 A 601 "
     model   vdw
     2.332 3.120
  ... (remaining 35210 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:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.380
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:6.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
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   0.047   4116  Z= 0.159
  Angle     :  0.574   8.841   5617  Z= 0.256
  Chirality :  0.044   0.223    632
  Planarity :  0.004   0.037    705
  Dihedral  : 10.449  77.848   1486
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.38), residues: 505
  helix:  1.01 (0.34), residues: 235
  sheet:  0.49 (0.59), residues: 68
  loop :  0.05 (0.48), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 332 
 TYR   0.009   0.001   TYR A 406 
 PHE   0.008   0.001   PHE A 426 
 TRP   0.008   0.001   TRP A 489 
 HIS   0.001   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4116)
  covalent geometry    : angle       0.57449 ( 5617)
  hydrogen bonds       : bond        0.20826 (  210)
  hydrogen bonds       : angle       7.78927 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7390 (tm-30)
REVERT: A   11 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6967 (mmt180)
REVERT: A  304 LEU cc_start: 0.8244 (tp) cc_final: 0.7965 (tp)
REVERT: A  310 TYR cc_start: 0.8544 (m-80) cc_final: 0.8283 (m-80)
REVERT: A  428 MET cc_start: 0.8714 (mtt) cc_final: 0.8471 (mtp)
REVERT: A  468 GLU cc_start: 0.8035 (tt0) cc_final: 0.7672 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.5574
  time to fit residues: 32.4601
Evaluate side-chains
  47 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0070
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.1404

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 244 ASN
A 464 GLN
A 488 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.119064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.085623 restraints weight = 4640.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.00
r_work: 0.2791 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2658 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4116  Z= 0.172
  Angle     :  0.580   5.990   5617  Z= 0.290
  Chirality :  0.045   0.181    632
  Planarity :  0.005   0.037    705
  Dihedral  :  7.283  57.119    599
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  4.90 %
    Favored  : 94.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.38), residues: 505
  helix:  1.12 (0.33), residues: 244
  sheet:  0.37 (0.57), residues: 64
  loop : -0.06 (0.49), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 289 
 TYR   0.010   0.001   TYR A 325 
 PHE   0.013   0.002   PHE A 174 
 TRP   0.009   0.001   TRP A 423 
 HIS   0.002   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 4116)
  covalent geometry    : angle       0.57967 ( 5617)
  hydrogen bonds       : bond        0.04465 (  210)
  hydrogen bonds       : angle       5.22718 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7542 (tm-30)
REVERT: A   11 ARG cc_start: 0.7562 (mmt180) cc_final: 0.7150 (mmt180)
REVERT: A  310 TYR cc_start: 0.8635 (m-80) cc_final: 0.8332 (m-80)
REVERT: A  468 GLU cc_start: 0.8254 (tt0) cc_final: 0.7879 (tt0)
  outliers start: 4
  outliers final: 1
  residues processed: 45
  average time/residue: 0.5714
  time to fit residues: 26.7496
Evaluate side-chains
  42 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 244 ASN
A 305 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.120415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.086888 restraints weight = 4620.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 2.00
r_work: 0.2815 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2683 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4116  Z= 0.132
  Angle     :  0.540   5.884   5617  Z= 0.267
  Chirality :  0.043   0.166    632
  Planarity :  0.004   0.037    705
  Dihedral  :  6.616  54.819    599
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  6.13 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.39), residues: 505
  helix:  1.24 (0.33), residues: 251
  sheet:  0.06 (0.57), residues: 67
  loop : -0.02 (0.51), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 289 
 TYR   0.009   0.001   TYR A 325 
 PHE   0.012   0.001   PHE A 174 
 TRP   0.010   0.001   TRP A 489 
 HIS   0.001   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4116)
  covalent geometry    : angle       0.54031 ( 5617)
  hydrogen bonds       : bond        0.03791 (  210)
  hydrogen bonds       : angle       4.71320 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: A   11 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7080 (mmt180)
REVERT: A  219 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8506 (pm20)
REVERT: A  310 TYR cc_start: 0.8651 (m-80) cc_final: 0.8359 (m-80)
REVERT: A  468 GLU cc_start: 0.8303 (tt0) cc_final: 0.8088 (tt0)
  outliers start: 5
  outliers final: 1
  residues processed: 48
  average time/residue: 0.5176
  time to fit residues: 25.8494
Evaluate side-chains
  43 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0870
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 244 ASN
A 314 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.120201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.086471 restraints weight = 4604.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 1.98
r_work: 0.2775 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4116  Z= 0.150
  Angle     :  0.552   5.945   5617  Z= 0.272
  Chirality :  0.044   0.169    632
  Planarity :  0.004   0.037    705
  Dihedral  :  6.518  58.210    599
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.60 %
    Favored  : 91.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.38), residues: 505
  helix:  1.27 (0.33), residues: 251
  sheet:  0.23 (0.56), residues: 63
  loop : -0.09 (0.50), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 289 
 TYR   0.010   0.001   TYR A 325 
 PHE   0.014   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 489 
 HIS   0.001   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4116)
  covalent geometry    : angle       0.55239 ( 5617)
  hydrogen bonds       : bond        0.03705 (  210)
  hydrogen bonds       : angle       4.62394 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: A   11 ARG cc_start: 0.7460 (mmt180) cc_final: 0.7043 (mmt180)
REVERT: A  219 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8542 (pm20)
REVERT: A  289 ARG cc_start: 0.6676 (mtm110) cc_final: 0.6437 (mtm110)
REVERT: A  310 TYR cc_start: 0.8650 (m-80) cc_final: 0.8406 (m-80)
REVERT: A  468 GLU cc_start: 0.8271 (tt0) cc_final: 0.8031 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 41
  average time/residue: 0.5494
  time to fit residues: 23.4877
Evaluate side-chains
  40 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0070
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.116982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.081563 restraints weight = 4661.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 2.15
r_work: 0.2759 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4116  Z= 0.122
  Angle     :  0.526   5.819   5617  Z= 0.258
  Chirality :  0.043   0.162    632
  Planarity :  0.004   0.037    705
  Dihedral  :  6.224  59.008    599
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.33 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.39), residues: 505
  helix:  1.39 (0.33), residues: 252
  sheet: -0.03 (0.56), residues: 67
  loop : -0.10 (0.51), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 289 
 TYR   0.009   0.001   TYR A 325 
 PHE   0.013   0.001   PHE A 174 
 TRP   0.011   0.001   TRP A 489 
 HIS   0.001   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4116)
  covalent geometry    : angle       0.52607 ( 5617)
  hydrogen bonds       : bond        0.03381 (  210)
  hydrogen bonds       : angle       4.46903 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: A   11 ARG cc_start: 0.7554 (mmt180) cc_final: 0.7149 (mmt180)
REVERT: A  219 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8543 (pm20)
REVERT: A  310 TYR cc_start: 0.8638 (m-80) cc_final: 0.8385 (m-80)
REVERT: A  468 GLU cc_start: 0.8387 (tt0) cc_final: 0.8116 (tt0)
REVERT: A  505 MET cc_start: 0.8077 (mmm) cc_final: 0.7759 (mmp)
  outliers start: 5
  outliers final: 3
  residues processed: 43
  average time/residue: 0.5886
  time to fit residues: 26.3607
Evaluate side-chains
  42 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0970
   chunk 41 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.121323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.087693 restraints weight = 4690.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.01
r_work: 0.2762 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2634 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4116  Z= 0.125
  Angle     :  0.531   5.831   5617  Z= 0.260
  Chirality :  0.043   0.164    632
  Planarity :  0.004   0.038    705
  Dihedral  :  6.196  59.981    599
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.58 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.38), residues: 505
  helix:  1.43 (0.33), residues: 252
  sheet: -0.04 (0.56), residues: 67
  loop : -0.15 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 289 
 TYR   0.009   0.001   TYR A 325 
 PHE   0.013   0.001   PHE A 174 
 TRP   0.010   0.001   TRP A 489 
 HIS   0.001   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4116)
  covalent geometry    : angle       0.53141 ( 5617)
  hydrogen bonds       : bond        0.03370 (  210)
  hydrogen bonds       : angle       4.44670 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: A   11 ARG cc_start: 0.7487 (mmt180) cc_final: 0.7075 (mmt180)
REVERT: A  219 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8511 (pm20)
REVERT: A  310 TYR cc_start: 0.8560 (m-80) cc_final: 0.8321 (m-80)
REVERT: A  468 GLU cc_start: 0.8308 (tt0) cc_final: 0.8075 (tt0)
REVERT: A  505 MET cc_start: 0.7922 (mmm) cc_final: 0.7647 (mmp)
  outliers start: 4
  outliers final: 2
  residues processed: 41
  average time/residue: 0.5821
  time to fit residues: 24.8276
Evaluate side-chains
  40 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0020
   chunk 0 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.8390

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

Flipped N/Q/H residues before XYZ refinement:
A  45 GLN
A 241 GLN
A 314 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.116250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.080740 restraints weight = 4714.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.15
r_work: 0.2753 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2620 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4116  Z= 0.134
  Angle     :  0.528   5.859   5617  Z= 0.260
  Chirality :  0.043   0.166    632
  Planarity :  0.004   0.038    705
  Dihedral  :  6.193  59.121    599
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.07 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.39), residues: 505
  helix:  1.40 (0.33), residues: 252
  sheet: -0.05 (0.56), residues: 67
  loop : -0.14 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 289 
 TYR   0.009   0.001   TYR A 325 
 PHE   0.013   0.001   PHE A 174 
 TRP   0.010   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4116)
  covalent geometry    : angle       0.52816 ( 5617)
  hydrogen bonds       : bond        0.03424 (  210)
  hydrogen bonds       : angle       4.45833 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: A   11 ARG cc_start: 0.7576 (mmt180) cc_final: 0.7179 (mmt180)
REVERT: A  219 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8539 (pm20)
REVERT: A  247 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7168 (ttpt)
REVERT: A  310 TYR cc_start: 0.8585 (m-80) cc_final: 0.8355 (m-80)
REVERT: A  468 GLU cc_start: 0.8402 (tt0) cc_final: 0.8186 (tt0)
REVERT: A  505 MET cc_start: 0.8046 (mmm) cc_final: 0.7724 (mmp)
  outliers start: 5
  outliers final: 2
  residues processed: 42
  average time/residue: 0.5565
  time to fit residues: 24.3104
Evaluate side-chains
  42 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 40 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 314 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.087554 restraints weight = 4635.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 1.99
r_work: 0.2754 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4116  Z= 0.127
  Angle     :  0.533   5.828   5617  Z= 0.262
  Chirality :  0.043   0.169    632
  Planarity :  0.005   0.048    705
  Dihedral  :  6.163  58.908    599
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.80 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.39), residues: 505
  helix:  1.46 (0.33), residues: 252
  sheet: -0.07 (0.56), residues: 67
  loop : -0.14 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 289 
 TYR   0.009   0.001   TYR A 325 
 PHE   0.013   0.001   PHE A 174 
 TRP   0.011   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4116)
  covalent geometry    : angle       0.53334 ( 5617)
  hydrogen bonds       : bond        0.03351 (  210)
  hydrogen bonds       : angle       4.43829 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7504 (tm-30)
REVERT: A   11 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7079 (mmt180)
REVERT: A  219 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8514 (pm20)
REVERT: A  247 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7091 (ttpt)
REVERT: A  310 TYR cc_start: 0.8544 (m-80) cc_final: 0.8319 (m-80)
REVERT: A  468 GLU cc_start: 0.8336 (tt0) cc_final: 0.8103 (tt0)
REVERT: A  505 MET cc_start: 0.7905 (mmm) cc_final: 0.7580 (mmp)
  outliers start: 3
  outliers final: 2
  residues processed: 40
  average time/residue: 0.5942
  time to fit residues: 24.6996
Evaluate side-chains
  41 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.0040
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 314 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.118065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.082744 restraints weight = 4783.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 2.17
r_work: 0.2793 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4116  Z= 0.110
  Angle     :  0.515   5.763   5617  Z= 0.252
  Chirality :  0.043   0.166    632
  Planarity :  0.004   0.042    705
  Dihedral  :  5.998  58.767    599
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.29 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.39), residues: 505
  helix:  1.56 (0.34), residues: 252
  sheet: -0.06 (0.56), residues: 67
  loop : -0.13 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 289 
 TYR   0.008   0.001   TYR A 406 
 PHE   0.012   0.001   PHE A 174 
 TRP   0.012   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4116)
  covalent geometry    : angle       0.51530 ( 5617)
  hydrogen bonds       : bond        0.03145 (  210)
  hydrogen bonds       : angle       4.35879 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   11 ARG cc_start: 0.7546 (mmt180) cc_final: 0.7164 (mmt180)
REVERT: A  219 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8545 (pm20)
REVERT: A  247 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7175 (ttpt)
REVERT: A  310 TYR cc_start: 0.8577 (m-80) cc_final: 0.8366 (m-80)
REVERT: A  468 GLU cc_start: 0.8410 (tt0) cc_final: 0.8106 (tt0)
REVERT: A  505 MET cc_start: 0.8005 (mmm) cc_final: 0.7736 (mmp)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 0.6006
  time to fit residues: 26.8188
Evaluate side-chains
  41 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0270
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 49 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 314 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.122799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.089233 restraints weight = 4601.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.00
r_work: 0.2831 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4116  Z= 0.111
  Angle     :  0.522   5.771   5617  Z= 0.255
  Chirality :  0.043   0.165    632
  Planarity :  0.004   0.038    705
  Dihedral  :  5.955  58.570    599
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.54 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.39), residues: 505
  helix:  1.58 (0.33), residues: 252
  sheet: -0.06 (0.56), residues: 67
  loop : -0.10 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 289 
 TYR   0.008   0.001   TYR A 325 
 PHE   0.011   0.001   PHE A 174 
 TRP   0.011   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4116)
  covalent geometry    : angle       0.52243 ( 5617)
  hydrogen bonds       : bond        0.03138 (  210)
  hydrogen bonds       : angle       4.33864 (  573)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   11 ARG cc_start: 0.7479 (mmt180) cc_final: 0.7096 (mmt180)
REVERT: A  219 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8527 (pm20)
REVERT: A  247 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7132 (ttpt)
REVERT: A  310 TYR cc_start: 0.8557 (m-80) cc_final: 0.8353 (m-80)
REVERT: A  468 GLU cc_start: 0.8368 (tt0) cc_final: 0.8056 (tt0)
REVERT: A  505 MET cc_start: 0.7977 (mmm) cc_final: 0.7683 (mmp)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 0.6324
  time to fit residues: 28.1790
Evaluate side-chains
  44 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  315 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 314 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.122427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.088768 restraints weight = 4609.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 2.00
r_work: 0.2840 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4116  Z= 0.119
  Angle     :  0.524   5.793   5617  Z= 0.256
  Chirality :  0.043   0.165    632
  Planarity :  0.004   0.038    705
  Dihedral  :  5.960  57.828    599
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.78 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.39), residues: 505
  helix:  1.53 (0.33), residues: 253
  sheet: -0.06 (0.56), residues: 67
  loop : -0.13 (0.50), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 289 
 TYR   0.009   0.001   TYR A 325 
 PHE   0.012   0.001   PHE A 174 
 TRP   0.010   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4116)
  covalent geometry    : angle       0.52446 ( 5617)
  hydrogen bonds       : bond        0.03200 (  210)
  hydrogen bonds       : angle       4.35456 (  573)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1665.95 seconds
wall clock time: 29 minutes 10.27 seconds (1750.27 seconds total)