Starting phenix.real_space_refine
on Wed Sep 17 06:45:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zwe_60524/09_2025/8zwe_60524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zwe_60524/09_2025/8zwe_60524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zwe_60524/09_2025/8zwe_60524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zwe_60524/09_2025/8zwe_60524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zwe_60524/09_2025/8zwe_60524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zwe_60524/09_2025/8zwe_60524.cif"
  }
  resolution = 3.0
  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=   0.081
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      41      5.16       5
     C    4125      2.51       5
     N    1072      2.21       5
     O    1227      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  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: 6465
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1556
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 13, 'TRANS': 187}
    Chain: "B"
      Number of atoms: 4881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4881
          Classifications: {'peptide': 593}
          Link IDs: {'PTRANS': 30, 'TRANS': 562}
    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
  Time building chain proxies: 1.54, per 1000 atoms: 0.24
  Number of scatterers: 6465
  At special positions: 0
  Unit cell: (72.812, 85.504, 116.232, 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      41     16.00
     O    1227      8.00
     N    1072      7.00
     C    4125      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 433 " - pdb=" SG  CYS A 486 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 445 " - pdb=" SG  CYS A 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 532 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 530 " - pdb=" SG  CYS B 542 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1001 " - " ASN B  53 "
      " NAG B1002 " - " ASN B 322 "
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 323.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1502

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      53.8% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 393 through 398
      removed outlier: 3.740A  pdb=" N   LEU A 397 " --> pdb=" O   PHE A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 425
      removed outlier: 3.705A  pdb=" N   LEU A 422 " --> pdb=" O   ASN A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 443
    Processing helix  chain 'A' and resid 461 through 465
    Processing helix  chain 'A' and resid 470 through 476
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'B' and resid 21 through 53
      removed outlier: 3.545A  pdb=" N   PHE B  28 " --> pdb=" O   LEU B  24 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR B  34 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   TYR B  41 " --> pdb=" O   GLU B  37 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLN B  42 " --> pdb=" O   GLU B  38 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN B  43 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 81
      removed outlier: 4.041A  pdb=" N   ILE B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN B  60 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS B  68 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TRP B  69 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 102
      removed outlier: 3.556A  pdb=" N   ALA B  99 " --> pdb=" O   ARG B  95 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 100 " --> pdb=" O   GLN B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 129
    Processing helix  chain 'B' and resid 147 through 154
    Processing helix  chain 'B' and resid 157 through 172
    Processing helix  chain 'B' and resid 176 through 193
      removed outlier: 3.561A  pdb=" N   GLU B 182 " --> pdb=" O   PRO B 178 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 218 through 249
      removed outlier: 3.771A  pdb=" N   LEU B 222 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ILE B 223 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU B 224 " --> pdb=" O   ASN B 220 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLN B 232 " --> pdb=" O   HIS B 228 " (cutoff:3.500A)
      Proline residue:  B 235  - end of helix
    Processing helix  chain 'B' and resid 265 through 267
      No H-bonds generated for 'chain 'B' and resid 265 through 267'
    Processing helix  chain 'B' and resid 275 through 282
      Proline residue:  B 280  - end of helix
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 303 through 317
      removed outlier: 3.980A  pdb=" N   ILE B 307 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   PHE B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 331
      removed outlier: 3.930A  pdb=" N   TRP B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN B 329 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 385
      removed outlier: 3.690A  pdb=" N   HIS B 373 " --> pdb=" O   PHE B 369 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   HIS B 378 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE B 379 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR B 385 " --> pdb=" O   TYR B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 413
      removed outlier: 3.879A  pdb=" N   GLY B 405 " --> pdb=" O   HIS B 401 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU B 406 " --> pdb=" O   GLU B 402 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE B 407 " --> pdb=" O   ALA B 403 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   MET B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   SER B 409 " --> pdb=" O   GLY B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 422
    Processing helix  chain 'B' and resid 433 through 443
    Processing helix  chain 'B' and resid 449 through 466
    Processing helix  chain 'B' and resid 472 through 484
    Processing helix  chain 'B' and resid 499 through 502
    Processing helix  chain 'B' and resid 503 through 508
    Processing helix  chain 'B' and resid 513 through 533
      removed outlier: 3.954A  pdb=" N   THR B 519 " --> pdb=" O   TYR B 515 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   PHE B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE B 532 " --> pdb=" O   ALA B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 547 through 559
      removed outlier: 3.581A  pdb=" N   MET B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 575
      removed outlier: 3.763A  pdb=" N   VAL B 573 " --> pdb=" O   ALA B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 588
      removed outlier: 3.610A  pdb=" N   PHE B 588 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 412
      removed outlier: 3.505A  pdb=" N   MET A 571 " --> pdb=" O   ALA A 490 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 417
    Processing sheet with id=AA3, first strand: chain 'A' and resid 518 through 521
      removed outlier: 3.867A  pdb=" N   GLY A 518 " --> pdb=" O   THR A 515 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR A 515 " --> pdb=" O   GLY A 518 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   THR A 559 " --> pdb=" O   THR A 509 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   CYS A 511 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL A 557 " --> pdb=" O   CYS A 511 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LYS A 513 " --> pdb=" O   TYR A 555 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   TYR A 555 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLY A 554 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 132
    Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263
      removed outlier: 5.799A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350

    293 hydrogen bonds defined for protein.
    840 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: 1.04

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2074
        1.34 -     1.46: 1656
        1.46 -     1.58: 2853
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 6649
  Sorted by residual:
  bond pdb=" C1  NAG B1001 "
       pdb=" O5  NAG B1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" C1  NAG B1002 "
       pdb=" O5  NAG B1002 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.87e+00
  bond pdb=" C5  NAG B1002 "
       pdb=" O5  NAG B1002 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C5  NAG B1001 "
       pdb=" O5  NAG B1001 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.11e+00
  bond pdb=" C3  NAG B1001 "
       pdb=" O3  NAG B1001 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.02e+00
  ... (remaining 6644 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 8684
        1.17 -     2.34: 273
        2.34 -     3.50: 58
        3.50 -     4.67: 13
        4.67 -     5.84: 9
  Bond angle restraints: 9037
  Sorted by residual:
  angle pdb=" N   ASP A 582 "
        pdb=" CA  ASP A 582 "
        pdb=" C   ASP A 582 "
      ideal   model   delta    sigma   weight residual
     107.99  113.83   -5.84 1.76e+00 3.23e-01 1.10e+01
  angle pdb=" C   ASP A 582 "
        pdb=" N   THR A 583 "
        pdb=" CA  THR A 583 "
      ideal   model   delta    sigma   weight residual
     121.54  127.03   -5.49 1.91e+00 2.74e-01 8.26e+00
  angle pdb=" N   THR A 583 "
        pdb=" CA  THR A 583 "
        pdb=" C   THR A 583 "
      ideal   model   delta    sigma   weight residual
     110.80  116.03   -5.23 2.13e+00 2.20e-01 6.02e+00
  angle pdb=" N   LYS B 234 "
        pdb=" CA  LYS B 234 "
        pdb=" C   LYS B 234 "
      ideal   model   delta    sigma   weight residual
     113.25  116.36   -3.11 1.30e+00 5.92e-01 5.71e+00
  angle pdb=" N   GLY A 580 "
        pdb=" CA  GLY A 580 "
        pdb=" C   GLY A 580 "
      ideal   model   delta    sigma   weight residual
     113.18  118.71   -5.53 2.37e+00 1.78e-01 5.44e+00
  ... (remaining 9032 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 3490
       17.78 -    35.56: 368
       35.56 -    53.34: 90
       53.34 -    71.11: 16
       71.11 -    88.89: 12
  Dihedral angle restraints: 3976
    sinusoidal: 1637
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" CA  THR A 581 "
           pdb=" C   THR A 581 "
           pdb=" N   ASP A 582 "
           pdb=" CA  ASP A 582 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.56  -21.44     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  TYR A 579 "
           pdb=" C   TYR A 579 "
           pdb=" N   GLY A 580 "
           pdb=" CA  GLY A 580 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.54  -20.46     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CB  CYS A 445 "
           pdb=" SG  CYS A 445 "
           pdb=" SG  CYS A 587 "
           pdb=" CB  CYS A 587 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.20  -32.20     1      1.00e+01 1.00e-02 1.48e+01
  ... (remaining 3973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 467
       0.024 -    0.047: 293
       0.047 -    0.071: 118
       0.071 -    0.095: 35
       0.095 -    0.118: 38
  Chirality restraints: 951
  Sorted by residual:
  chirality pdb=" CA  ILE A 574 "
            pdb=" N   ILE A 574 "
            pdb=" C   ILE A 574 "
            pdb=" CB  ILE A 574 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.49e-01
  chirality pdb=" CA  VAL B 487 "
            pdb=" N   VAL B 487 "
            pdb=" C   VAL B 487 "
            pdb=" CB  VAL B 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  LYS B 234 "
            pdb=" N   LYS B 234 "
            pdb=" C   LYS B 234 "
            pdb=" CB  LYS B 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.36e-01
  ... (remaining 948 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 530 "    0.041 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO A 531 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 531 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 531 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 459 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   TRP B 459 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   TRP B 459 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG B 460 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 458 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   LYS B 458 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LYS B 458 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TRP B 459 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 916
        2.76 -     3.29: 5898
        3.29 -     3.83: 10727
        3.83 -     4.36: 12818
        4.36 -     4.90: 22468
  Nonbonded interactions: 52827
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 183 "
            pdb=" OD1 ASP B 509 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" O   ILE B 358 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ILE B  59 "
            pdb=" ND2 ASN B  63 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OH  TYR B 237 "
            pdb=" O   VAL B 485 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NH2 ARG B 245 "
            pdb=" O   PHE B 603 "
     model   vdw
     2.316 3.120
  ... (remaining 52822 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:             1.850
  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:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.730
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
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      :  0.003   0.030   6657  Z= 0.129
  Angle     :  0.543   5.839   9055  Z= 0.294
  Chirality :  0.040   0.118    951
  Planarity :  0.004   0.062   1168
  Dihedral  : 16.061  88.892   2456
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.80 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.69 %
    Favored  : 86.31 %
  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: -0.05 (0.30), residues: 790
  helix:  0.44 (0.27), residues: 391
  sheet:  0.14 (0.51), residues: 79
  loop : -0.53 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  98 
 TYR   0.009   0.001   TYR B 497 
 PHE   0.023   0.001   PHE A 407 
 TRP   0.016   0.001   TRP B 165 
 HIS   0.002   0.001   HIS A 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6649)
  covalent geometry    : angle       0.53654 ( 9037)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       0.61787 (   12)
  hydrogen bonds       : bond        0.17652 (  293)
  hydrogen bonds       : angle       6.40669 (  840)
  link_NAG-ASN         : bond        0.00086 (    2)
  link_NAG-ASN         : angle       3.16313 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  460 MET cc_start: 0.7008 (mtt) cc_final: 0.6666 (mtp)
REVERT: B  150 ASP cc_start: 0.7939 (t0) cc_final: 0.7601 (t0)
  outliers start: 0
  outliers final: 1
  residues processed: 86
  average time/residue: 0.6147
  time to fit residues: 55.5487
Evaluate side-chains
  78 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
B 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.167035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.122984 restraints weight = 7475.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.45
r_work: 0.3008 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.0956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6657  Z= 0.191
  Angle     :  0.574   6.559   9055  Z= 0.296
  Chirality :  0.043   0.130    951
  Planarity :  0.005   0.058   1168
  Dihedral  :  5.316  41.226    912
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.80 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.98 %
    Favored  : 84.45 %
  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:  0.14 (0.30), residues: 790
  helix:  0.74 (0.27), residues: 398
  sheet:  0.29 (0.53), residues: 79
  loop : -0.69 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 169 
 TYR   0.017   0.002   TYR B 385 
 PHE   0.013   0.002   PHE B 308 
 TRP   0.015   0.001   TRP B 478 
 HIS   0.006   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 6649)
  covalent geometry    : angle       0.56711 ( 9037)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       0.73269 (   12)
  hydrogen bonds       : bond        0.05458 (  293)
  hydrogen bonds       : angle       4.58432 (  840)
  link_NAG-ASN         : bond        0.00138 (    2)
  link_NAG-ASN         : angle       3.39976 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  460 MET cc_start: 0.7075 (mtt) cc_final: 0.6628 (mtp)
REVERT: B  150 ASP cc_start: 0.8204 (t0) cc_final: 0.7751 (t0)
REVERT: B  288 LYS cc_start: 0.7757 (mmtp) cc_final: 0.7539 (mttm)
  outliers start: 18
  outliers final: 9
  residues processed: 95
  average time/residue: 0.5298
  time to fit residues: 53.0531
Evaluate side-chains
  89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  597 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 3 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0370
   chunk 59 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    1.4862

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
A 584 ASN
B 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.167374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.121659 restraints weight = 7394.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.74
r_work: 0.2943 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6657  Z= 0.146
  Angle     :  0.521   6.031   9055  Z= 0.269
  Chirality :  0.041   0.132    951
  Planarity :  0.004   0.052   1168
  Dihedral  :  4.843  38.250    910
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.12 %
    Favored  : 83.59 %
  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:  0.37 (0.30), residues: 790
  helix:  1.06 (0.27), residues: 392
  sheet:  0.28 (0.54), residues: 79
  loop : -0.72 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 169 
 TYR   0.013   0.001   TYR B 385 
 PHE   0.019   0.002   PHE A 407 
 TRP   0.015   0.001   TRP B 163 
 HIS   0.004   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6649)
  covalent geometry    : angle       0.51377 ( 9037)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       0.68982 (   12)
  hydrogen bonds       : bond        0.04791 (  293)
  hydrogen bonds       : angle       4.39134 (  840)
  link_NAG-ASN         : bond        0.00085 (    2)
  link_NAG-ASN         : angle       3.30404 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  460 MET cc_start: 0.6934 (mtt) cc_final: 0.6510 (mtp)
REVERT: B  150 ASP cc_start: 0.8109 (t0) cc_final: 0.7598 (t0)
REVERT: B  288 LYS cc_start: 0.7712 (mmtp) cc_final: 0.7490 (mttm)
  outliers start: 16
  outliers final: 8
  residues processed: 97
  average time/residue: 0.5528
  time to fit residues: 56.5150
Evaluate side-chains
  87 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  578 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0060
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 52 optimal weight:    0.2980
   chunk 68 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
B 420 ASN
B 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.168588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.124976 restraints weight = 7540.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.13
r_work: 0.2980 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6657  Z= 0.096
  Angle     :  0.471   5.373   9055  Z= 0.242
  Chirality :  0.039   0.130    951
  Planarity :  0.004   0.044   1168
  Dihedral  :  4.443  33.901    910
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.84 %
    Favored  : 82.60 %
  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:  0.71 (0.30), residues: 790
  helix:  1.33 (0.27), residues: 392
  sheet:  0.30 (0.53), residues: 85
  loop : -0.51 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 169 
 TYR   0.010   0.001   TYR A 505 
 PHE   0.020   0.001   PHE A 407 
 TRP   0.018   0.001   TRP B 163 
 HIS   0.003   0.001   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6649)
  covalent geometry    : angle       0.46486 ( 9037)
  SS BOND              : bond        0.00215 (    6)
  SS BOND              : angle       0.63793 (   12)
  hydrogen bonds       : bond        0.03817 (  293)
  hydrogen bonds       : angle       4.23440 (  840)
  link_NAG-ASN         : bond        0.00070 (    2)
  link_NAG-ASN         : angle       2.83423 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  460 MET cc_start: 0.6997 (mtt) cc_final: 0.6631 (mtp)
REVERT: B  150 ASP cc_start: 0.8105 (t0) cc_final: 0.7579 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 93
  average time/residue: 0.5772
  time to fit residues: 56.5700
Evaluate side-chains
  89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain B residue   62 MET
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  581 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 65 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
B 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.169539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.126507 restraints weight = 7617.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.19
r_work: 0.2989 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6657  Z= 0.107
  Angle     :  0.476   5.090   9055  Z= 0.245
  Chirality :  0.039   0.130    951
  Planarity :  0.004   0.043   1168
  Dihedral  :  4.368  34.597    910
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.83 %
    Favored  : 81.60 %
  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:  0.79 (0.30), residues: 790
  helix:  1.43 (0.27), residues: 392
  sheet:  0.34 (0.53), residues: 85
  loop : -0.52 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 113 
 TYR   0.010   0.001   TYR B 385 
 PHE   0.021   0.001   PHE A 407 
 TRP   0.015   0.001   TRP B 163 
 HIS   0.004   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6649)
  covalent geometry    : angle       0.47075 ( 9037)
  SS BOND              : bond        0.00247 (    6)
  SS BOND              : angle       0.61339 (   12)
  hydrogen bonds       : bond        0.04023 (  293)
  hydrogen bonds       : angle       4.15949 (  840)
  link_NAG-ASN         : bond        0.00051 (    2)
  link_NAG-ASN         : angle       2.81934 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  460 MET cc_start: 0.6972 (mtt) cc_final: 0.6570 (mtp)
REVERT: B  150 ASP cc_start: 0.8148 (t0) cc_final: 0.7650 (t0)
REVERT: B  552 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7738 (mp10)
  outliers start: 18
  outliers final: 9
  residues processed: 94
  average time/residue: 0.5416
  time to fit residues: 53.6936
Evaluate side-chains
  89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  597 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0770
   chunk 10 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    2.2146

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.166512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120797 restraints weight = 7578.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.77
r_work: 0.2955 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6657  Z= 0.192
  Angle     :  0.559   6.279   9055  Z= 0.286
  Chirality :  0.043   0.130    951
  Planarity :  0.004   0.046   1168
  Dihedral  :  4.817  41.650    910
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.41 %
    Favored  : 81.46 %
  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:  0.56 (0.31), residues: 790
  helix:  1.24 (0.27), residues: 392
  sheet:  0.45 (0.53), residues: 84
  loop : -0.70 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 113 
 TYR   0.016   0.002   TYR B 385 
 PHE   0.023   0.002   PHE A 407 
 TRP   0.017   0.001   TRP B 163 
 HIS   0.006   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 6649)
  covalent geometry    : angle       0.55218 ( 9037)
  SS BOND              : bond        0.00366 (    6)
  SS BOND              : angle       0.70165 (   12)
  hydrogen bonds       : bond        0.05178 (  293)
  hydrogen bonds       : angle       4.29236 (  840)
  link_NAG-ASN         : bond        0.00194 (    2)
  link_NAG-ASN         : angle       3.35172 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  396 MET cc_start: 0.4423 (OUTLIER) cc_final: 0.4020 (mpt)
REVERT: A  460 MET cc_start: 0.6955 (mtt) cc_final: 0.6571 (mtp)
REVERT: A  529 TYR cc_start: 0.7028 (m-80) cc_final: 0.6808 (m-80)
REVERT: B  150 ASP cc_start: 0.8178 (t0) cc_final: 0.7630 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 97
  average time/residue: 0.5617
  time to fit residues: 57.4501
Evaluate side-chains
  97 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  531 GLN
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  597 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
B 472 GLN
B 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.165681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.120322 restraints weight = 7499.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.68
r_work: 0.2967 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6657  Z= 0.203
  Angle     :  0.569   6.577   9055  Z= 0.292
  Chirality :  0.043   0.132    951
  Planarity :  0.004   0.048   1168
  Dihedral  :  4.942  41.604    910
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.98 %
    Favored  : 80.31 %
  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:  0.40 (0.30), residues: 790
  helix:  1.13 (0.27), residues: 392
  sheet:  0.30 (0.52), residues: 84
  loop : -0.79 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 169 
 TYR   0.017   0.002   TYR B 385 
 PHE   0.024   0.002   PHE A 407 
 TRP   0.015   0.002   TRP B 163 
 HIS   0.006   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 6649)
  covalent geometry    : angle       0.56189 ( 9037)
  SS BOND              : bond        0.00372 (    6)
  SS BOND              : angle       0.74970 (   12)
  hydrogen bonds       : bond        0.05225 (  293)
  hydrogen bonds       : angle       4.32485 (  840)
  link_NAG-ASN         : bond        0.00206 (    2)
  link_NAG-ASN         : angle       3.54243 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  396 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.4331 (mpt)
REVERT: A  460 MET cc_start: 0.7047 (mtt) cc_final: 0.6658 (mtp)
REVERT: A  529 TYR cc_start: 0.7058 (m-80) cc_final: 0.6847 (m-80)
REVERT: B  150 ASP cc_start: 0.8161 (t0) cc_final: 0.7620 (t0)
REVERT: B  288 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7521 (mmtp)
REVERT: B  474 MET cc_start: 0.8803 (mmp) cc_final: 0.8554 (mmp)
  outliers start: 19
  outliers final: 12
  residues processed: 92
  average time/residue: 0.5623
  time to fit residues: 54.4690
Evaluate side-chains
  90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  531 GLN
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  597 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 19 optimal weight:   30.0000
   chunk 8 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
B 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.167273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.122297 restraints weight = 7446.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.71
r_work: 0.2994 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6657  Z= 0.143
  Angle     :  0.520   5.653   9055  Z= 0.268
  Chirality :  0.041   0.132    951
  Planarity :  0.004   0.048   1168
  Dihedral  :  4.697  38.000    910
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.12 %
    Favored  : 80.17 %
  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:  0.52 (0.30), residues: 790
  helix:  1.25 (0.27), residues: 392
  sheet:  0.27 (0.52), residues: 84
  loop : -0.74 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 169 
 TYR   0.013   0.001   TYR B 385 
 PHE   0.022   0.002   PHE A 407 
 TRP   0.018   0.001   TRP B 163 
 HIS   0.005   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6649)
  covalent geometry    : angle       0.51298 ( 9037)
  SS BOND              : bond        0.00283 (    6)
  SS BOND              : angle       0.66439 (   12)
  hydrogen bonds       : bond        0.04531 (  293)
  hydrogen bonds       : angle       4.23842 (  840)
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       3.21293 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  396 MET cc_start: 0.4809 (OUTLIER) cc_final: 0.4350 (mpt)
REVERT: A  460 MET cc_start: 0.7029 (mtt) cc_final: 0.6670 (mtp)
REVERT: B  150 ASP cc_start: 0.8170 (t0) cc_final: 0.7631 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 100
  average time/residue: 0.5760
  time to fit residues: 60.5223
Evaluate side-chains
  98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  531 GLN
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  597 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 479 GLN
A 504 ASN
A 524 ASN
B 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.165648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.120527 restraints weight = 7556.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.74
r_work: 0.2933 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6657  Z= 0.193
  Angle     :  0.585   8.642   9055  Z= 0.297
  Chirality :  0.043   0.132    951
  Planarity :  0.004   0.049   1168
  Dihedral  :  4.880  40.724    910
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.55 %
    Favored  : 80.03 %
  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:  0.42 (0.30), residues: 790
  helix:  1.16 (0.27), residues: 392
  sheet:  0.29 (0.52), residues: 84
  loop : -0.80 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 169 
 TYR   0.016   0.002   TYR B 385 
 PHE   0.024   0.002   PHE A 407 
 TRP   0.014   0.001   TRP B 163 
 HIS   0.006   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 6649)
  covalent geometry    : angle       0.57823 ( 9037)
  SS BOND              : bond        0.00360 (    6)
  SS BOND              : angle       0.72195 (   12)
  hydrogen bonds       : bond        0.05128 (  293)
  hydrogen bonds       : angle       4.26912 (  840)
  link_NAG-ASN         : bond        0.00216 (    2)
  link_NAG-ASN         : angle       3.40479 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  396 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.4588 (mpt)
REVERT: A  460 MET cc_start: 0.7082 (mtt) cc_final: 0.6705 (mtp)
REVERT: B  150 ASP cc_start: 0.8163 (t0) cc_final: 0.7622 (t0)
REVERT: B  288 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7482 (mmtp)
  outliers start: 17
  outliers final: 12
  residues processed: 90
  average time/residue: 0.5505
  time to fit residues: 52.1993
Evaluate side-chains
  92 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  531 GLN
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  597 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 4 optimal weight:    0.0370
   chunk 73 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0870
   chunk 26 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
B 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.170933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.127352 restraints weight = 7427.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.03
r_work: 0.3012 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6657  Z= 0.100
  Angle     :  0.511   7.916   9055  Z= 0.259
  Chirality :  0.040   0.131    951
  Planarity :  0.004   0.045   1168
  Dihedral  :  4.414  33.603    910
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.40 %
    Favored  : 79.74 %
  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:  0.72 (0.30), residues: 790
  helix:  1.38 (0.27), residues: 392
  sheet:  0.29 (0.52), residues: 85
  loop : -0.58 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 169 
 TYR   0.009   0.001   TYR A 505 
 PHE   0.025   0.001   PHE A 407 
 TRP   0.022   0.001   TRP B 163 
 HIS   0.002   0.001   HIS A 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 6649)
  covalent geometry    : angle       0.50645 ( 9037)
  SS BOND              : bond        0.00170 (    6)
  SS BOND              : angle       0.55604 (   12)
  hydrogen bonds       : bond        0.03644 (  293)
  hydrogen bonds       : angle       4.13038 (  840)
  link_NAG-ASN         : bond        0.00039 (    2)
  link_NAG-ASN         : angle       2.67915 (    6)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  396 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4762 (mpt)
REVERT: A  458 THR cc_start: 0.7027 (m) cc_final: 0.6820 (m)
REVERT: A  460 MET cc_start: 0.7072 (mtt) cc_final: 0.6765 (mtp)
REVERT: B  150 ASP cc_start: 0.8120 (t0) cc_final: 0.7638 (t0)
REVERT: B  360 MET cc_start: 0.8989 (ttm) cc_final: 0.8670 (ttp)
  outliers start: 13
  outliers final: 8
  residues processed: 87
  average time/residue: 0.5695
  time to fit residues: 52.3402
Evaluate side-chains
  86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  531 GLN
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  581 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0670
   chunk 10 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    2.0126

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 524 ASN
B 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.167593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.124406 restraints weight = 7523.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.07
r_work: 0.3038 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6657  Z= 0.175
  Angle     :  0.574   8.449   9055  Z= 0.290
  Chirality :  0.042   0.131    951
  Planarity :  0.004   0.046   1168
  Dihedral  :  4.715  39.812    910
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.12 %
    Favored  : 79.32 %
  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:  0.57 (0.30), residues: 790
  helix:  1.28 (0.27), residues: 392
  sheet:  0.36 (0.52), residues: 84
  loop : -0.72 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 169 
 TYR   0.015   0.001   TYR B 385 
 PHE   0.027   0.002   PHE A 407 
 TRP   0.019   0.001   TRP B 163 
 HIS   0.006   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6649)
  covalent geometry    : angle       0.56874 ( 9037)
  SS BOND              : bond        0.00355 (    6)
  SS BOND              : angle       0.66229 (   12)
  hydrogen bonds       : bond        0.04955 (  293)
  hydrogen bonds       : angle       4.21395 (  840)
  link_NAG-ASN         : bond        0.00167 (    2)
  link_NAG-ASN         : angle       3.15025 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2629.80 seconds
wall clock time: 45 minutes 33.25 seconds (2733.25 seconds total)