Starting phenix.real_space_refine
on Wed Sep 17 04:03:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zxm_60544/09_2025/8zxm_60544.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zxm_60544/09_2025/8zxm_60544.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zxm_60544/09_2025/8zxm_60544.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zxm_60544/09_2025/8zxm_60544.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zxm_60544/09_2025/8zxm_60544.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zxm_60544/09_2025/8zxm_60544.cif"
  }
  resolution = 3.39
  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=   0.001 sd=   0.099
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: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2419      2.51       5
     N     591      2.21       5
     O     640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3665
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3625
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 25, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'URC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.13, per 1000 atoms: 0.31
  Number of scatterers: 3665
  At special positions: 0
  Unit cell: (90.304, 59.76, 70.384, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     640      8.00
     N     591      7.00
     C    2419      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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A  90 "
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 156.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  856

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 0 sheets defined
      85.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 68 through 75
      removed outlier: 3.603A  pdb=" N   ASN A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 98
      removed outlier: 3.932A  pdb=" N   ALA A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ARG A  96 " --> pdb=" O   SER A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 132
      removed outlier: 4.973A  pdb=" N   PHE A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   ALA A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   MET A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 144
      removed outlier: 3.640A  pdb=" N   THR A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU A 141 " --> pdb=" O   ARG A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 156
      removed outlier: 3.750A  pdb=" N   LEU A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
    Processing helix  chain 'A' and resid 164 through 193
      removed outlier: 3.810A  pdb=" N   LEU A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
      Proline residue:  A 186  - end of helix
    Processing helix  chain 'A' and resid 200 through 219
      removed outlier: 3.772A  pdb=" N   VAL A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE A 208 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 237
      removed outlier: 4.147A  pdb=" N   PHE A 235 " --> pdb=" O   TRP A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 3.952A  pdb=" N   PHE A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 282 through 297
    Processing helix  chain 'A' and resid 303 through 308
    Processing helix  chain 'A' and resid 310 through 312
      No H-bonds generated for 'chain 'A' and resid 310 through 312'
    Processing helix  chain 'A' and resid 313 through 330
      removed outlier: 3.545A  pdb=" N   VAL A 320 " --> pdb=" O   GLN A 316 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   CYS A 326 " --> pdb=" O   VAL A 322 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN A 328 " --> pdb=" O   MET A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 338
    Processing helix  chain 'A' and resid 338 through 347
      removed outlier: 3.640A  pdb=" N   GLY A 347 " --> pdb=" O   PHE A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 370
      removed outlier: 3.560A  pdb=" N   LEU A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER A 359 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   THR A 360 " --> pdb=" O   VAL A 356 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLY A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLY A 362 " --> pdb=" O   LEU A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 379
      removed outlier: 3.732A  pdb=" N   GLU A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   HIS A 377 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY A 379 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 404
      removed outlier: 3.895A  pdb=" N   PHE A 388 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLY A 392 " --> pdb=" O   PHE A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 428
      removed outlier: 3.526A  pdb=" N   SER A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A 416 " --> pdb=" O   PRO A 412 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 432
      removed outlier: 4.150A  pdb=" N   GLY A 432 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 429 through 432'
    Processing helix  chain 'A' and resid 433 through 441
      removed outlier: 4.051A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 467
      removed outlier: 4.107A  pdb=" N   ILE A 452 " --> pdb=" O   PRO A 448 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASN A 458 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 477
    Processing helix  chain 'A' and resid 478 through 480
      No H-bonds generated for 'chain 'A' and resid 478 through 480'
    Processing helix  chain 'A' and resid 481 through 499
    Processing helix  chain 'A' and resid 506 through 519
      removed outlier: 3.512A  pdb=" N   GLN A 512 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LYS A 516 " --> pdb=" O   GLN A 512 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ARG A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)

    237 hydrogen bonds defined for protein.
    708 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: 0.48

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 673
        1.33 -     1.46: 1140
        1.46 -     1.58: 1924
        1.58 -     1.71: 0
        1.71 -     1.83: 22
  Bond restraints: 3759
  Sorted by residual:
  bond pdb=" C   LEU A 499 "
       pdb=" N   PRO A 500 "
    ideal  model  delta    sigma   weight residual
    1.329  1.366 -0.037 1.25e-02 6.40e+03 8.68e+00
  bond pdb=" C   ARG A 381 "
       pdb=" N   PRO A 382 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 9.40e-03 1.13e+04 7.54e+00
  bond pdb=" C   ILE A 348 "
       pdb=" N   PRO A 349 "
    ideal  model  delta    sigma   weight residual
    1.329  1.359 -0.030 1.18e-02 7.18e+03 6.28e+00
  bond pdb=" C   TRP A 231 "
       pdb=" N   PRO A 232 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.032 1.28e-02 6.10e+03 6.12e+00
  bond pdb=" C   TYR A  71 "
       pdb=" O   TYR A  71 "
    ideal  model  delta    sigma   weight residual
    1.236  1.208  0.028 1.19e-02 7.06e+03 5.60e+00
  ... (remaining 3754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 3998
        1.48 -     2.96: 940
        2.96 -     4.44: 162
        4.44 -     5.92: 22
        5.92 -     7.40: 2
  Bond angle restraints: 5124
  Sorted by residual:
  angle pdb=" CA  PHE A  88 "
        pdb=" CB  PHE A  88 "
        pdb=" CG  PHE A  88 "
      ideal   model   delta    sigma   weight residual
     113.80  118.53   -4.73 1.00e+00 1.00e+00 2.24e+01
  angle pdb=" CA  PHE A 337 "
        pdb=" CB  PHE A 337 "
        pdb=" CG  PHE A 337 "
      ideal   model   delta    sigma   weight residual
     113.80  118.24   -4.44 1.00e+00 1.00e+00 1.97e+01
  angle pdb=" N   GLU A 306 "
        pdb=" CA  GLU A 306 "
        pdb=" CB  GLU A 306 "
      ideal   model   delta    sigma   weight residual
     110.26  104.30    5.96 1.49e+00 4.50e-01 1.60e+01
  angle pdb=" CA  PHE A 117 "
        pdb=" CB  PHE A 117 "
        pdb=" CG  PHE A 117 "
      ideal   model   delta    sigma   weight residual
     113.80  117.72   -3.92 1.00e+00 1.00e+00 1.54e+01
  angle pdb=" C   GLN A 446 "
        pdb=" N   ARG A 447 "
        pdb=" CA  ARG A 447 "
      ideal   model   delta    sigma   weight residual
     120.09  124.62   -4.53 1.25e+00 6.40e-01 1.32e+01
  ... (remaining 5119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 2034
       17.85 -    35.69: 131
       35.69 -    53.53: 27
       53.53 -    71.37: 8
       71.37 -    89.21: 4
  Dihedral angle restraints: 2204
    sinusoidal: 861
      harmonic: 1343
  Sorted by residual:
  dihedral pdb=" CA  ASN A 145 "
           pdb=" C   ASN A 145 "
           pdb=" N   GLY A 146 "
           pdb=" CA  GLY A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.32   25.68     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  LEU A 373 "
           pdb=" C   LEU A 373 "
           pdb=" N   VAL A 374 "
           pdb=" CA  VAL A 374 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.45   19.55     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  VAL A 313 "
           pdb=" C   VAL A 313 "
           pdb=" N   ARG A 314 "
           pdb=" CA  ARG A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.47  -18.53     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 282
       0.049 -    0.098: 175
       0.098 -    0.147: 110
       0.147 -    0.196: 31
       0.196 -    0.245: 8
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.31e+01
  chirality pdb=" CA  TRP A 231 "
            pdb=" N   TRP A 231 "
            pdb=" C   TRP A 231 "
            pdb=" CB  TRP A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  PHE A 394 "
            pdb=" N   PHE A 394 "
            pdb=" C   PHE A 394 "
            pdb=" CB  PHE A 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 603 not shown)

  Planarity restraints: 631
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "    0.077 2.00e-02 2.50e+03   6.44e-02 5.18e+01
        pdb=" C7  NAG B   1 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "    0.056 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "   -0.106 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 494 "   -0.044 2.00e-02 2.50e+03   2.34e-02 1.09e+01
        pdb=" CG  TYR A 494 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 494 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 494 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 494 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 494 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 494 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 494 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 507 "    0.038 2.00e-02 2.50e+03   2.12e-02 8.97e+00
        pdb=" CG  TYR A 507 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 507 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 507 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 507 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 507 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 507 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 507 "    0.019 2.00e-02 2.50e+03
  ... (remaining 628 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 1914
        3.01 -     3.48: 3719
        3.48 -     3.96: 5919
        3.96 -     4.43: 6733
        4.43 -     4.90: 10892
  Nonbonded interactions: 29177
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 102 "
            pdb=" OG1 THR A 105 "
     model   vdw
     2.540 3.040
  nonbonded pdb=" OG1 THR A 506 "
            pdb=" OE1 GLU A 509 "
     model   vdw
     2.575 3.040
  nonbonded pdb=" N   PRO A 194 "
            pdb=" O   PRO A 194 "
     model   vdw
     2.610 2.496
  nonbonded pdb=" C   SER A 255 "
            pdb=" OG  SER A 255 "
     model   vdw
     2.620 2.616
  nonbonded pdb=" O   ILE A 335 "
            pdb=" OG1 THR A 339 "
     model   vdw
     2.623 3.040
  ... (remaining 29172 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.540
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
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      :  0.009   0.048   3761  Z= 0.585
  Angle     :  1.316   8.806   5130  Z= 0.876
  Chirality :  0.083   0.245    606
  Planarity :  0.009   0.071    630
  Dihedral  : 13.578  89.214   1348
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 0.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  4.12 %
    Favored  : 94.07 %
  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: -3.84 (0.32), residues: 469
  helix: -2.68 (0.21), residues: 355
  sheet:  None (None), residues: 0
  loop : -1.14 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.003   ARG A  96 
 TYR   0.044   0.009   TYR A 494 
 PHE   0.039   0.008   PHE A 463 
 TRP   0.030   0.008   TRP A 110 
 HIS   0.012   0.004   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00894 ( 3759)
  covalent geometry    : angle       1.30724 ( 5124)
  hydrogen bonds       : bond        0.23139 (  237)
  hydrogen bonds       : angle       9.75867 (  708)
  link_BETA1-4         : bond        0.04780 (    1)
  link_BETA1-4         : angle       5.38277 (    3)
  link_NAG-ASN         : bond        0.01894 (    1)
  link_NAG-ASN         : angle       3.59071 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   99 ARG cc_start: 0.4769 (pmt170) cc_final: 0.4153 (ptt180)
REVERT: A  174 MET cc_start: 0.8207 (tpp) cc_final: 0.7687 (tpp)
REVERT: A  444 GLN cc_start: 0.6815 (mm110) cc_final: 0.6575 (tp-100)
  outliers start: 7
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0968
  time to fit residues: 6.1238
Evaluate side-chains
  36 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  213 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0570
   overall best weight:    0.6098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.158404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118038 restraints weight = 3915.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.28
r_work: 0.3267 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3761  Z= 0.155
  Angle     :  0.656   6.639   5130  Z= 0.342
  Chirality :  0.045   0.155    606
  Planarity :  0.005   0.029    630
  Dihedral  :  5.718  59.992    554
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  :  5.93 %
    Favored  : 91.75 %
  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: -1.29 (0.38), residues: 469
  helix: -0.77 (0.26), residues: 368
  sheet:  None (None), residues: 0
  loop : -0.46 (0.68), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  95 
 TYR   0.012   0.002   TYR A 355 
 PHE   0.014   0.002   PHE A 273 
 TRP   0.017   0.002   TRP A 231 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3759)
  covalent geometry    : angle       0.65145 ( 5124)
  hydrogen bonds       : bond        0.05443 (  237)
  hydrogen bonds       : angle       5.06802 (  708)
  link_BETA1-4         : bond        0.00358 (    1)
  link_BETA1-4         : angle       1.86478 (    3)
  link_NAG-ASN         : bond        0.00126 (    1)
  link_NAG-ASN         : angle       2.62924 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.6362 (tttp)
REVERT: A  263 LYS cc_start: 0.5548 (mmtt) cc_final: 0.5176 (mmtt)
REVERT: A  391 MET cc_start: 0.6971 (mtt) cc_final: 0.6713 (mtt)
  outliers start: 9
  outliers final: 5
  residues processed: 39
  average time/residue: 0.0558
  time to fit residues: 2.9372
Evaluate side-chains
  34 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  501 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   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 145 ASN
A 377 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.143400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.103087 restraints weight = 3804.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.25
r_work: 0.3014 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3761  Z= 0.131
  Angle     :  0.578   5.687   5130  Z= 0.294
  Chirality :  0.043   0.146    606
  Planarity :  0.005   0.031    630
  Dihedral  :  5.043  57.073    553
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  7.99 %
    Favored  : 90.21 %
  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: -0.21 (0.40), residues: 469
  helix:  0.06 (0.28), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.36 (0.70), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  95 
 TYR   0.008   0.001   TYR A  73 
 PHE   0.012   0.001   PHE A 441 
 TRP   0.014   0.002   TRP A 231 
 HIS   0.001   0.000   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3759)
  covalent geometry    : angle       0.57468 ( 5124)
  hydrogen bonds       : bond        0.04148 (  237)
  hydrogen bonds       : angle       4.26777 (  708)
  link_BETA1-4         : bond        0.00417 (    1)
  link_BETA1-4         : angle       1.40007 (    3)
  link_NAG-ASN         : bond        0.00152 (    1)
  link_NAG-ASN         : angle       2.10170 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  306 GLU cc_start: 0.7954 (tp30) cc_final: 0.6559 (mt-10)
REVERT: A  440 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6404 (tt0)
  outliers start: 7
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0530
  time to fit residues: 2.8388
Evaluate side-chains
  32 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  501 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:    0.2980
   chunk 8 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0980
   chunk 45 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
A 377 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.145941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.105199 restraints weight = 3764.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.27
r_work: 0.3043 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3761  Z= 0.109
  Angle     :  0.520   5.205   5130  Z= 0.262
  Chirality :  0.041   0.142    606
  Planarity :  0.004   0.033    630
  Dihedral  :  3.878  14.802    547
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  8.76 %
    Favored  : 88.66 %
  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:  0.33 (0.41), residues: 469
  helix:  0.47 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.29 (0.72), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 505 
 TYR   0.007   0.001   TYR A 327 
 PHE   0.010   0.001   PHE A 441 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3759)
  covalent geometry    : angle       0.51714 ( 5124)
  hydrogen bonds       : bond        0.03556 (  237)
  hydrogen bonds       : angle       3.95876 (  708)
  link_BETA1-4         : bond        0.00379 (    1)
  link_BETA1-4         : angle       1.20155 (    3)
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       1.95735 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  440 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6345 (tt0)
  outliers start: 10
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0418
  time to fit residues: 2.4465
Evaluate side-chains
  32 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  384 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.143443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.102686 restraints weight = 3850.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.34
r_work: 0.3013 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3761  Z= 0.129
  Angle     :  0.541   5.249   5130  Z= 0.273
  Chirality :  0.043   0.144    606
  Planarity :  0.004   0.034    630
  Dihedral  :  3.856  14.213    547
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 10.57 %
    Favored  : 87.37 %
  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:  0.47 (0.41), residues: 469
  helix:  0.63 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.49 (0.69), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 505 
 TYR   0.008   0.001   TYR A 327 
 PHE   0.011   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3759)
  covalent geometry    : angle       0.53890 ( 5124)
  hydrogen bonds       : bond        0.03746 (  237)
  hydrogen bonds       : angle       3.91409 (  708)
  link_BETA1-4         : bond        0.00354 (    1)
  link_BETA1-4         : angle       1.17382 (    3)
  link_NAG-ASN         : bond        0.00173 (    1)
  link_NAG-ASN         : angle       1.97455 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   99 ARG cc_start: 0.5958 (pmt170) cc_final: 0.5112 (ptt180)
REVERT: A  509 GLU cc_start: 0.7065 (mp0) cc_final: 0.6784 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 40
  average time/residue: 0.1083
  time to fit residues: 5.1692
Evaluate side-chains
  38 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  465 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 24 optimal weight:    8.9990
   chunk 13 optimal weight:    0.5980
   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 284 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.142991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.102618 restraints weight = 3898.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.30
r_work: 0.3014 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3761  Z= 0.129
  Angle     :  0.538   5.232   5130  Z= 0.270
  Chirality :  0.042   0.144    606
  Planarity :  0.004   0.034    630
  Dihedral  :  3.807  14.135    547
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 10.57 %
    Favored  : 86.60 %
  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:  0.63 (0.41), residues: 469
  helix:  0.77 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.52 (0.69), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.008   0.001   TYR A 327 
 PHE   0.011   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3759)
  covalent geometry    : angle       0.53550 ( 5124)
  hydrogen bonds       : bond        0.03663 (  237)
  hydrogen bonds       : angle       3.89656 (  708)
  link_BETA1-4         : bond        0.00272 (    1)
  link_BETA1-4         : angle       1.07962 (    3)
  link_NAG-ASN         : bond        0.00168 (    1)
  link_NAG-ASN         : angle       1.92848 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   99 ARG cc_start: 0.5877 (pmt170) cc_final: 0.4970 (ptt180)
REVERT: A  509 GLU cc_start: 0.7050 (mp0) cc_final: 0.6627 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 44
  average time/residue: 0.0891
  time to fit residues: 4.8159
Evaluate side-chains
  43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  465 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.167400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127573 restraints weight = 4028.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.22
r_work: 0.3386 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3761  Z= 0.129
  Angle     :  0.538   5.235   5130  Z= 0.270
  Chirality :  0.042   0.143    606
  Planarity :  0.004   0.034    630
  Dihedral  :  3.763  14.090    547
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 11.08 %
    Favored  : 85.82 %
  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:  0.79 (0.41), residues: 469
  helix:  0.89 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.53 (0.69), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 505 
 TYR   0.008   0.001   TYR A 327 
 PHE   0.011   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3759)
  covalent geometry    : angle       0.53533 ( 5124)
  hydrogen bonds       : bond        0.03664 (  237)
  hydrogen bonds       : angle       3.87250 (  708)
  link_BETA1-4         : bond        0.00264 (    1)
  link_BETA1-4         : angle       1.03576 (    3)
  link_NAG-ASN         : bond        0.00210 (    1)
  link_NAG-ASN         : angle       1.90983 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  284 GLN cc_start: 0.6226 (mp-120) cc_final: 0.5915 (mp10)
REVERT: A  509 GLU cc_start: 0.7380 (mp0) cc_final: 0.7064 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 43
  average time/residue: 0.0771
  time to fit residues: 4.1878
Evaluate side-chains
  43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  468 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.165369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.126987 restraints weight = 3975.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.12
r_work: 0.3387 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3761  Z= 0.133
  Angle     :  0.538   5.260   5130  Z= 0.270
  Chirality :  0.042   0.143    606
  Planarity :  0.004   0.034    630
  Dihedral  :  3.741  14.066    547
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 11.60 %
    Favored  : 85.82 %
  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 (0.41), residues: 469
  helix:  0.93 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.46 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 505 
 TYR   0.008   0.001   TYR A 355 
 PHE   0.011   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3759)
  covalent geometry    : angle       0.53614 ( 5124)
  hydrogen bonds       : bond        0.03706 (  237)
  hydrogen bonds       : angle       3.85454 (  708)
  link_BETA1-4         : bond        0.00307 (    1)
  link_BETA1-4         : angle       1.04714 (    3)
  link_NAG-ASN         : bond        0.00258 (    1)
  link_NAG-ASN         : angle       1.94428 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   99 ARG cc_start: 0.6306 (pmt170) cc_final: 0.5484 (ptt180)
REVERT: A  257 ARG cc_start: 0.6436 (tmt170) cc_final: 0.6220 (tmt170)
REVERT: A  284 GLN cc_start: 0.6236 (mp-120) cc_final: 0.5927 (mp10)
REVERT: A  509 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7031 (mp0)
  outliers start: 10
  outliers final: 9
  residues processed: 42
  average time/residue: 0.0938
  time to fit residues: 4.8179
Evaluate side-chains
  44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  509 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0070
   chunk 40 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.169079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.129575 restraints weight = 3954.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.18
r_work: 0.3409 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3761  Z= 0.111
  Angle     :  0.511   5.214   5130  Z= 0.256
  Chirality :  0.041   0.142    606
  Planarity :  0.004   0.034    630
  Dihedral  :  3.616  13.795    547
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.37 %
    Favored  : 85.57 %
  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:  1.08 (0.41), residues: 469
  helix:  1.10 (0.29), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.41 (0.70), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 505 
 TYR   0.007   0.001   TYR A  73 
 PHE   0.009   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3759)
  covalent geometry    : angle       0.50871 ( 5124)
  hydrogen bonds       : bond        0.03342 (  237)
  hydrogen bonds       : angle       3.74502 (  708)
  link_BETA1-4         : bond        0.00318 (    1)
  link_BETA1-4         : angle       1.00340 (    3)
  link_NAG-ASN         : bond        0.00120 (    1)
  link_NAG-ASN         : angle       1.92093 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   99 ARG cc_start: 0.6324 (pmt170) cc_final: 0.5500 (ptt180)
REVERT: A  284 GLN cc_start: 0.6228 (mp-120) cc_final: 0.5927 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0774
  time to fit residues: 3.9915
Evaluate side-chains
  37 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  465 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 43 optimal weight:    0.3980
   chunk 14 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.167911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130322 restraints weight = 3963.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.22
r_work: 0.3417 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3761  Z= 0.118
  Angle     :  0.522   5.214   5130  Z= 0.263
  Chirality :  0.042   0.142    606
  Planarity :  0.004   0.034    630
  Dihedral  :  3.617  13.672    547
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.63 %
    Favored  : 85.57 %
  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:  1.13 (0.41), residues: 469
  helix:  1.13 (0.29), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.41 (0.69), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 505 
 TYR   0.007   0.001   TYR A  73 
 PHE   0.010   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3759)
  covalent geometry    : angle       0.51982 ( 5124)
  hydrogen bonds       : bond        0.03447 (  237)
  hydrogen bonds       : angle       3.74910 (  708)
  link_BETA1-4         : bond        0.00326 (    1)
  link_BETA1-4         : angle       1.02923 (    3)
  link_NAG-ASN         : bond        0.00170 (    1)
  link_NAG-ASN         : angle       1.93418 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   99 ARG cc_start: 0.6349 (pmt170) cc_final: 0.5508 (ptt180)
REVERT: A  160 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7639 (mt0)
REVERT: A  284 GLN cc_start: 0.6266 (mp-120) cc_final: 0.5978 (mp10)
REVERT: A  384 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6659 (tp)
  outliers start: 7
  outliers final: 6
  residues processed: 39
  average time/residue: 0.0802
  time to fit residues: 3.9245
Evaluate side-chains
  38 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  465 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    0.2980
   chunk 30 optimal weight:    0.0770
   overall best weight:    0.5138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.167997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.131298 restraints weight = 3882.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.09
r_work: 0.3437 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3761  Z= 0.111
  Angle     :  0.511   5.211   5130  Z= 0.257
  Chirality :  0.041   0.142    606
  Planarity :  0.004   0.034    630
  Dihedral  :  3.568  13.570    547
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 12.37 %
    Favored  : 85.31 %
  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:  1.23 (0.41), residues: 469
  helix:  1.21 (0.29), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.37 (0.70), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 505 
 TYR   0.007   0.001   TYR A  73 
 PHE   0.009   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.001   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3759)
  covalent geometry    : angle       0.50854 ( 5124)
  hydrogen bonds       : bond        0.03287 (  237)
  hydrogen bonds       : angle       3.71571 (  708)
  link_BETA1-4         : bond        0.00328 (    1)
  link_BETA1-4         : angle       1.01060 (    3)
  link_NAG-ASN         : bond        0.00156 (    1)
  link_NAG-ASN         : angle       1.94261 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 978.36 seconds
wall clock time: 17 minutes 28.83 seconds (1048.83 seconds total)