Starting phenix.real_space_refine
on Tue Mar 11 19:54:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qsq_18639/03_2025/8qsq_18639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qsq_18639/03_2025/8qsq_18639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qsq_18639/03_2025/8qsq_18639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qsq_18639/03_2025/8qsq_18639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qsq_18639/03_2025/8qsq_18639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qsq_18639/03_2025/8qsq_18639.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
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      37      5.16       5
     C    4174      2.51       5
     N    1073      2.21       5
     O    1228      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6512
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1566
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.60, per 1000 atoms: 0.71
  Number of scatterers: 6512
  At special positions: 0
  Unit cell: (74.46, 99.28, 116.8, 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      37     16.00
     O    1228      8.00
     N    1073      7.00
     C    4174      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 344 " - pdb=" SG  CYS B 361 " 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 B 801 " - " ASN B 322 "
      " NAG B 802 " - " ASN B 546 "
      " NAG B 803 " - " ASN B 432 "
      " NAG B 804 " - " ASN B  53 "
      " NAG B 805 " - " ASN B  90 "
      " NAG B 806 " - " ASN B 103 "
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 943.0 milliseconds
  

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 7 sheets defined
      58.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 4.330A  pdb=" N   VAL A 338 " --> pdb=" O   PRO A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 363
      No H-bonds generated for 'chain 'A' and resid 361 through 363'
    Processing helix  chain 'A' and resid 364 through 369
      removed outlier: 3.896A  pdb=" N   ALA A 369 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 387
      removed outlier: 4.951A  pdb=" N   ASN A 385 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 3.854A  pdb=" N   SER A 405 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'B' and resid 20 through 52
      removed outlier: 3.751A  pdb=" N   HIS B  34 " --> pdb=" O   ASP B  30 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP B  38 " --> pdb=" O   HIS B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 81
      removed outlier: 3.505A  pdb=" N   VAL B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 83
      No H-bonds generated for 'chain 'B' and resid 82 through 83'
    Processing helix  chain 'B' and resid 84 through 88
    Processing helix  chain 'B' and resid 90 through 102
      removed outlier: 3.539A  pdb=" N   GLN B  96 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.620A  pdb=" N   SER B 106 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 130
    Processing helix  chain 'B' and resid 146 through 155
    Processing helix  chain 'B' and resid 157 through 172
      removed outlier: 3.651A  pdb=" N   ARG B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 194
      Proline residue:  B 178  - end of helix
      removed outlier: 3.543A  pdb=" N   GLU B 182 " --> pdb=" O   PRO B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 204
    Processing helix  chain 'B' and resid 205 through 208
    Processing helix  chain 'B' and resid 218 through 252
      removed outlier: 3.757A  pdb=" N   LEU B 222 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE B 223 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU B 224 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU B 232 " --> pdb=" O   HIS B 228 " (cutoff:3.500A)
      Proline residue:  B 235  - end of helix
    Processing helix  chain 'B' and resid 275 through 277
      No H-bonds generated for 'chain 'B' and resid 275 through 277'
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 303 through 318
      removed outlier: 3.615A  pdb=" N   VAL B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 331
      removed outlier: 3.568A  pdb=" N   TRP B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 385
      removed outlier: 3.526A  pdb=" N   HIS B 373 " --> pdb=" O   PHE B 369 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS B 378 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 388
      No H-bonds generated for 'chain 'B' and resid 386 through 388'
    Processing helix  chain 'B' and resid 389 through 393
    Processing helix  chain 'B' and resid 399 through 413
      removed outlier: 3.803A  pdb=" N   MET B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   SER B 409 " --> pdb=" O   GLY B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 421
    Processing helix  chain 'B' and resid 431 through 446
      removed outlier: 3.651A  pdb=" N   THR B 445 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 465
    Processing helix  chain 'B' and resid 469 through 471
      No H-bonds generated for 'chain 'B' and resid 469 through 471'
    Processing helix  chain 'B' and resid 472 through 484
    Processing helix  chain 'B' and resid 498 through 502
    Processing helix  chain 'B' and resid 503 through 508
    Processing helix  chain 'B' and resid 513 through 533
      removed outlier: 3.702A  pdb=" N   PHE B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 547 through 559
      removed outlier: 4.104A  pdb=" N   MET B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 575
      removed outlier: 3.841A  pdb=" N   VAL B 573 " --> pdb=" O   ALA B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 588
    Processing helix  chain 'B' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355
    Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359
      removed outlier: 7.322A  pdb=" N   CYS A 358 " --> pdb=" O   CYS A 521 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 133
    Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263
      removed outlier: 5.865A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 352
      removed outlier: 6.138A  pdb=" N   ASP B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    879 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: 1.85

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2073
        1.34 -     1.46: 1700
        1.46 -     1.58: 2870
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6701
  Sorted by residual:
  bond pdb=" C1  NAG B 806 "
       pdb=" O5  NAG B 806 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.07e+00
  bond pdb=" C1  NAG B 801 "
       pdb=" O5  NAG B 801 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" C1  NAG B 805 "
       pdb=" O5  NAG B 805 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.06e+00
  bond pdb=" C1  NAG B 803 "
       pdb=" O5  NAG B 803 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG B 802 "
       pdb=" O5  NAG B 802 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.86e+00
  ... (remaining 6696 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 8845
        1.12 -     2.24: 193
        2.24 -     3.36: 56
        3.36 -     4.48: 10
        4.48 -     5.60: 5
  Bond angle restraints: 9109
  Sorted by residual:
  angle pdb=" CA  LYS A 478 "
        pdb=" CB  LYS A 478 "
        pdb=" CG  LYS A 478 "
      ideal   model   delta    sigma   weight residual
     114.10  118.03   -3.93 2.00e+00 2.50e-01 3.85e+00
  angle pdb=" C   CYS A 477 "
        pdb=" N   LYS A 478 "
        pdb=" CA  LYS A 478 "
      ideal   model   delta    sigma   weight residual
     121.54  125.22   -3.68 1.91e+00 2.74e-01 3.72e+00
  angle pdb=" N   VAL B 573 "
        pdb=" CA  VAL B 573 "
        pdb=" C   VAL B 573 "
      ideal   model   delta    sigma   weight residual
     111.67  109.98    1.69 9.50e-01 1.11e+00 3.17e+00
  angle pdb=" CA  TYR B 385 "
        pdb=" CB  TYR B 385 "
        pdb=" CG  TYR B 385 "
      ideal   model   delta    sigma   weight residual
     113.90  117.08   -3.18 1.80e+00 3.09e-01 3.12e+00
  angle pdb=" CA  HIS A 515 "
        pdb=" C   HIS A 515 "
        pdb=" N   ALA A 516 "
      ideal   model   delta    sigma   weight residual
     118.22  116.47    1.75 1.03e+00 9.43e-01 2.89e+00
  ... (remaining 9104 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 3811
       17.29 -    34.57: 166
       34.57 -    51.86: 37
       51.86 -    69.14: 10
       69.14 -    86.43: 4
  Dihedral angle restraints: 4028
    sinusoidal: 1704
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" N   LYS B 476 "
           pdb=" CA  LYS B 476 "
           pdb=" CB  LYS B 476 "
           pdb=" CG  LYS B 476 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.49   59.49     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   HIS B 401 "
           pdb=" CA  HIS B 401 "
           pdb=" CB  HIS B 401 "
           pdb=" CG  HIS B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -128.43  -51.57     3      1.50e+01 4.44e-03 9.03e+00
  dihedral pdb=" N   GLU B  56 "
           pdb=" CA  GLU B  56 "
           pdb=" CB  GLU B  56 "
           pdb=" CG  GLU B  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -131.28  -48.72     3      1.50e+01 4.44e-03 8.68e+00
  ... (remaining 4025 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 879
       0.071 -    0.142: 83
       0.142 -    0.214: 1
       0.214 -    0.285: 1
       0.285 -    0.356: 1
  Chirality restraints: 965
  Sorted by residual:
  chirality pdb=" C1  NAG B 806 "
            pdb=" ND2 ASN B 103 "
            pdb=" C2  NAG B 806 "
            pdb=" O5  NAG B 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.76    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" C1  NAG B 801 "
            pdb=" ND2 ASN B 322 "
            pdb=" C2  NAG B 801 "
            pdb=" O5  NAG B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C1  NAG B 805 "
            pdb=" ND2 ASN B  90 "
            pdb=" C2  NAG B 805 "
            pdb=" O5  NAG B 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.61    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 962 not shown)

  Planarity restraints: 1177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 103 "   -0.037 2.00e-02 2.50e+03   4.04e-02 2.05e+01
        pdb=" CG  ASN B 103 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 103 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 103 "    0.065 2.00e-02 2.50e+03
        pdb=" C1  NAG B 806 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 432 "   -0.026 2.00e-02 2.50e+03   2.75e-02 9.44e+00
        pdb=" CG  ASN B 432 "    0.011 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 432 "    0.006 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 432 "    0.043 2.00e-02 2.50e+03
        pdb=" C1  NAG B 803 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 322 "    0.016 2.00e-02 2.50e+03   1.77e-02 3.91e+00
        pdb=" CG  ASN B 322 "   -0.006 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 322 "   -0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 322 "   -0.029 2.00e-02 2.50e+03
        pdb=" C1  NAG B 801 "    0.021 2.00e-02 2.50e+03
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1662
        2.79 -     3.32: 6121
        3.32 -     3.85: 11106
        3.85 -     4.37: 13721
        4.37 -     4.90: 22537
  Nonbonded interactions: 55147
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 607 "
            pdb=" OD1 ASP B 609 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" NZ  LYS B 288 "
            pdb=" OD2 ASP B 431 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   ASP B 499 "
            pdb=" OG  SER B 502 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG1 THR B 276 "
            pdb=" OG1 THR B 445 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NZ  LYS B  31 "
            pdb=" OE2 GLU B  35 "
     model   vdw
     2.330 3.120
  ... (remaining 55142 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 group one per residue
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:             1.120
  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:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.900
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
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      :  0.002   0.035   6701  Z= 0.149
  Angle     :  0.462   5.602   9109  Z= 0.232
  Chirality :  0.043   0.356    965
  Planarity :  0.003   0.031   1171
  Dihedral  : 10.949  86.426   2515
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  4.17 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.28), residues: 787
  helix: -1.37 (0.21), residues: 390
  sheet:  0.15 (0.74), residues: 49
  loop : -0.35 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 478 
 HIS   0.003   0.001   HIS B 241 
 PHE   0.006   0.001   PHE B 523 
 TYR   0.015   0.001   TYR B 385 
 ARG   0.002   0.000   ARG B 245 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  367 ASN cc_start: 0.8572 (m-40) cc_final: 0.8165 (t0)
REVERT: A  415 ILE cc_start: 0.8974 (mm) cc_final: 0.8569 (pt)
REVERT: B   56 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8579 (pm20)
REVERT: B  213 ASP cc_start: 0.9163 (m-30) cc_final: 0.8412 (p0)
REVERT: B  322 ASN cc_start: 0.4723 (OUTLIER) cc_final: 0.4312 (p0)
REVERT: B  323 MET cc_start: 0.6861 (mmp) cc_final: 0.6469 (mmp)
REVERT: B  455 MET cc_start: 0.5113 (tmt) cc_final: 0.3262 (ttp)
REVERT: B  474 MET cc_start: -0.0441 (mmm) cc_final: -0.2701 (mmp)
REVERT: B  572 ASN cc_start: 0.7642 (m-40) cc_final: 0.7303 (t0)
  outliers start: 8
  outliers final: 1
  residues processed: 91
  average time/residue: 0.2288
  time to fit residues: 26.7739
Evaluate side-chains
  42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 GLU
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  401 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:   30.0000
   chunk 45 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0270
   overall best weight:    6.6046

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

Flipped N/Q/H residues before XYZ refinement:
A 483 ASN
** B  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
B 210 ASN
B 340 GLN
B 552 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.048322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.039689 restraints weight = 95996.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.040598 restraints weight = 57610.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.041191 restraints weight = 39566.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6701  Z= 0.310
  Angle     :  0.709   7.502   9109  Z= 0.379
  Chirality :  0.045   0.198    965
  Planarity :  0.006   0.057   1171
  Dihedral  :  5.935  58.211    991
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.36 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.29), residues: 787
  helix:  0.38 (0.24), residues: 390
  sheet:  0.11 (0.74), residues: 49
  loop : -0.30 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 328 
 HIS   0.008   0.002   HIS A 501 
 PHE   0.018   0.002   PHE A 368 
 TYR   0.029   0.002   TYR B 385 
 ARG   0.006   0.001   ARG A 354 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  123 MET cc_start: 0.4801 (mtp) cc_final: 0.4598 (ptm)
REVERT: B  455 MET cc_start: 0.4498 (tmt) cc_final: 0.3263 (ttp)
REVERT: B  572 ASN cc_start: 0.8587 (m-40) cc_final: 0.8083 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 50
  average time/residue: 0.1829
  time to fit residues: 13.0907
Evaluate side-chains
  38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  341 LYS
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  522 GLN
Chi-restraints excluded: chain B residue  534 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 49 optimal weight:   50.0000
   chunk 77 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:   30.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 483 ASN
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.049326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.041289 restraints weight = 86543.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.042183 restraints weight = 51619.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.042751 restraints weight = 34769.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6701  Z= 0.162
  Angle     :  0.542   7.526   9109  Z= 0.283
  Chirality :  0.041   0.163    965
  Planarity :  0.004   0.031   1171
  Dihedral  :  4.389  22.664    984
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.22 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.30), residues: 787
  helix:  0.83 (0.25), residues: 400
  sheet:  0.45 (0.74), residues: 51
  loop : -0.19 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 328 
 HIS   0.007   0.001   HIS A 501 
 PHE   0.013   0.001   PHE B 315 
 TYR   0.016   0.001   TYR B 385 
 ARG   0.003   0.000   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8427 (mpp) cc_final: 0.7821 (ppp)
REVERT: B  455 MET cc_start: 0.3789 (tmt) cc_final: 0.3320 (ttp)
REVERT: B  474 MET cc_start: -0.2478 (mmp) cc_final: -0.2763 (mmp)
REVERT: B  494 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8281 (p0)
REVERT: B  557 MET cc_start: 0.6009 (tmm) cc_final: 0.5758 (tmm)
REVERT: B  572 ASN cc_start: 0.8607 (m-40) cc_final: 0.8035 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 42
  average time/residue: 0.1474
  time to fit residues: 9.5599
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 58 optimal weight:   40.0000
   chunk 59 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 77 optimal weight:    7.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  96 GLN
B 305 GLN
** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.046915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.038944 restraints weight = 89131.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.039777 restraints weight = 52924.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.040319 restraints weight = 35468.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.5719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6701  Z= 0.238
  Angle     :  0.611   6.333   9109  Z= 0.322
  Chirality :  0.043   0.212    965
  Planarity :  0.004   0.030   1171
  Dihedral  :  5.058  31.837    984
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  9.35 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.29), residues: 787
  helix:  0.52 (0.25), residues: 402
  sheet:  0.56 (0.79), residues: 48
  loop : -0.25 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 478 
 HIS   0.008   0.002   HIS B 535 
 PHE   0.017   0.002   PHE A 368 
 TYR   0.017   0.002   TYR B 385 
 ARG   0.008   0.001   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 29
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8353 (mpp) cc_final: 0.7920 (ppp)
REVERT: B  270 MET cc_start: 0.0947 (mmm) cc_final: 0.0375 (mmm)
REVERT: B  323 MET cc_start: 0.7801 (mmt) cc_final: 0.7471 (mmt)
REVERT: B  455 MET cc_start: 0.4093 (tmt) cc_final: 0.3531 (ttp)
REVERT: B  474 MET cc_start: -0.1501 (mmp) cc_final: -0.1963 (mmp)
REVERT: B  485 VAL cc_start: 0.6429 (OUTLIER) cc_final: 0.5620 (t)
REVERT: B  494 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7987 (p0)
REVERT: B  572 ASN cc_start: 0.8720 (m-40) cc_final: 0.8383 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 45
  average time/residue: 0.1385
  time to fit residues: 9.8959
Evaluate side-chains
  40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 63 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   30.0000
   chunk 8 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.045736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.037910 restraints weight = 90722.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.038755 restraints weight = 52561.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.039319 restraints weight = 34773.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.7072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6701  Z= 0.300
  Angle     :  0.700   8.164   9109  Z= 0.370
  Chirality :  0.045   0.254    965
  Planarity :  0.005   0.036   1171
  Dihedral  :  5.523  26.834    984
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 22.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.36 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.29), residues: 787
  helix: -0.01 (0.25), residues: 403
  sheet:  0.93 (0.75), residues: 45
  loop : -0.64 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 275 
 HIS   0.009   0.002   HIS B 535 
 PHE   0.024   0.002   PHE B 315 
 TYR   0.017   0.002   TYR B 385 
 ARG   0.006   0.001   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 26
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8430 (mpp) cc_final: 0.7793 (ppp)
REVERT: B  339 VAL cc_start: 0.2891 (OUTLIER) cc_final: 0.2312 (m)
REVERT: B  455 MET cc_start: 0.5390 (tmt) cc_final: 0.4957 (ttp)
REVERT: B  462 MET cc_start: 0.6280 (mmp) cc_final: 0.5919 (mmp)
REVERT: B  474 MET cc_start: -0.1709 (mmp) cc_final: -0.2657 (mmt)
REVERT: B  485 VAL cc_start: 0.6282 (OUTLIER) cc_final: 0.5177 (t)
REVERT: B  572 ASN cc_start: 0.9015 (m-40) cc_final: 0.8651 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 41
  average time/residue: 0.1485
  time to fit residues: 9.4486
Evaluate side-chains
  38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  534 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 52 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 63 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 51 optimal weight:   50.0000
   chunk 10 optimal weight:   30.0000
   chunk 29 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 277 ASN
** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 524 GLN
B 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.045430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.037718 restraints weight = 90537.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.038528 restraints weight = 52754.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.039068 restraints weight = 35079.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.7642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6701  Z= 0.283
  Angle     :  0.648   5.979   9109  Z= 0.346
  Chirality :  0.044   0.270    965
  Planarity :  0.005   0.033   1171
  Dihedral  :  5.307  22.587    984
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 22.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.94 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.29), residues: 787
  helix: -0.00 (0.25), residues: 401
  sheet:  0.93 (0.74), residues: 45
  loop : -0.78 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 275 
 HIS   0.008   0.002   HIS A 501 
 PHE   0.015   0.002   PHE A 368 
 TYR   0.015   0.002   TYR B  50 
 ARG   0.007   0.001   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 24
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8344 (mpp) cc_final: 0.7935 (ppp)
REVERT: B  339 VAL cc_start: 0.3261 (OUTLIER) cc_final: 0.2996 (t)
REVERT: B  455 MET cc_start: 0.5789 (tmt) cc_final: 0.5333 (ttp)
REVERT: B  474 MET cc_start: -0.1682 (mmp) cc_final: -0.2554 (mmt)
REVERT: B  485 VAL cc_start: 0.6492 (OUTLIER) cc_final: 0.5703 (t)
REVERT: B  572 ASN cc_start: 0.9065 (m-40) cc_final: 0.8646 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 42
  average time/residue: 0.1661
  time to fit residues: 10.6887
Evaluate side-chains
  38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 23
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  534 LYS
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 58 optimal weight:    7.9990
   chunk 56 optimal weight:    0.0870
   chunk 23 optimal weight:    5.9990
   chunk 71 optimal weight:    7.9990
   chunk 34 optimal weight:   30.0000
   chunk 62 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 43 optimal weight:    0.2980
   chunk 6 optimal weight:    4.9990
   overall best weight:    3.8764

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

Flipped N/Q/H residues before XYZ refinement:
B 472 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.045981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.038312 restraints weight = 90065.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.039156 restraints weight = 51841.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.039712 restraints weight = 33996.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.7652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6701  Z= 0.201
  Angle     :  0.582   6.657   9109  Z= 0.306
  Chirality :  0.042   0.234    965
  Planarity :  0.004   0.034   1171
  Dihedral  :  4.930  19.356    984
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.94 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.29), residues: 787
  helix:  0.23 (0.25), residues: 399
  sheet:  1.00 (0.75), residues: 46
  loop : -0.72 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 478 
 HIS   0.007   0.002   HIS A 501 
 PHE   0.019   0.002   PHE B 315 
 TYR   0.015   0.001   TYR B 237 
 ARG   0.005   0.001   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 24
  time to evaluate  : 0.874 
Fit side-chains
REVERT: B  271 TRP cc_start: 0.0496 (OUTLIER) cc_final: -0.1727 (m-90)
REVERT: B  455 MET cc_start: 0.5037 (tmt) cc_final: 0.4759 (ttp)
REVERT: B  474 MET cc_start: -0.1801 (mmp) cc_final: -0.2628 (mmt)
REVERT: B  485 VAL cc_start: 0.6357 (OUTLIER) cc_final: 0.5520 (t)
REVERT: B  494 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7946 (p0)
REVERT: B  572 ASN cc_start: 0.9009 (m-40) cc_final: 0.8661 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 38
  average time/residue: 0.1647
  time to fit residues: 9.6539
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 23
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  271 TRP
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  534 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 59 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0010
   chunk 47 optimal weight:    0.8980
   overall best weight:    2.7792

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.045858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.038015 restraints weight = 90230.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.038868 restraints weight = 52602.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.039429 restraints weight = 34934.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.7664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6701  Z= 0.168
  Angle     :  0.567   8.658   9109  Z= 0.293
  Chirality :  0.042   0.205    965
  Planarity :  0.004   0.032   1171
  Dihedral  :  4.580  18.630    984
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.66 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.30), residues: 787
  helix:  0.34 (0.26), residues: 408
  sheet:  1.45 (0.76), residues: 45
  loop : -0.55 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 478 
 HIS   0.006   0.001   HIS A 501 
 PHE   0.021   0.001   PHE B 315 
 TYR   0.013   0.001   TYR B 237 
 ARG   0.004   0.001   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.764 
Fit side-chains
REVERT: B  271 TRP cc_start: -0.0182 (OUTLIER) cc_final: -0.2349 (m-90)
REVERT: B  455 MET cc_start: 0.6085 (tmt) cc_final: 0.5512 (ppp)
REVERT: B  474 MET cc_start: -0.1903 (mmp) cc_final: -0.2673 (mmt)
REVERT: B  480 MET cc_start: 0.7386 (ttm) cc_final: 0.7180 (ttt)
REVERT: B  494 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8303 (p0)
REVERT: B  572 ASN cc_start: 0.9026 (m-40) cc_final: 0.8732 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 34
  average time/residue: 0.1514
  time to fit residues: 8.1380
Evaluate side-chains
  32 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  271 TRP
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 68 optimal weight:    8.9990
   chunk 70 optimal weight:    8.9990
   chunk 5 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    3.0986

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.045787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.037944 restraints weight = 91020.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.038775 restraints weight = 53014.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.039321 restraints weight = 35222.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.7823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6701  Z= 0.176
  Angle     :  0.567   7.510   9109  Z= 0.296
  Chirality :  0.042   0.207    965
  Planarity :  0.004   0.032   1171
  Dihedral  :  4.608  19.225    984
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.66 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.30), residues: 787
  helix:  0.39 (0.25), residues: 408
  sheet:  1.44 (0.76), residues: 45
  loop : -0.48 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 478 
 HIS   0.006   0.001   HIS A 501 
 PHE   0.011   0.001   PHE B 315 
 TYR   0.015   0.001   TYR B 385 
 ARG   0.004   0.001   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: B  271 TRP cc_start: 0.0247 (OUTLIER) cc_final: -0.2123 (m-90)
REVERT: B  455 MET cc_start: 0.6237 (tmt) cc_final: 0.5573 (ttp)
REVERT: B  474 MET cc_start: -0.1931 (mmp) cc_final: -0.2737 (mmt)
REVERT: B  572 ASN cc_start: 0.8911 (m-40) cc_final: 0.8655 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 34
  average time/residue: 0.1498
  time to fit residues: 8.0181
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  271 TRP
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 49 optimal weight:    0.3980
   chunk 42 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    4.6788

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.045687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.038075 restraints weight = 91005.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.038893 restraints weight = 53367.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.039436 restraints weight = 35600.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.8224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6701  Z= 0.225
  Angle     :  0.631  10.480   9109  Z= 0.327
  Chirality :  0.043   0.237    965
  Planarity :  0.004   0.036   1171
  Dihedral  :  5.071  27.266    984
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.81 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.30), residues: 787
  helix:  0.25 (0.25), residues: 408
  sheet:  1.12 (0.74), residues: 45
  loop : -0.54 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 275 
 HIS   0.007   0.002   HIS A 501 
 PHE   0.013   0.002   PHE A 368 
 TYR   0.014   0.002   TYR B 516 
 ARG   0.005   0.001   ARG A 494 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.786 
Fit side-chains
REVERT: B  271 TRP cc_start: 0.1280 (OUTLIER) cc_final: -0.1177 (m-90)
REVERT: B  455 MET cc_start: 0.6095 (tmt) cc_final: 0.5880 (ttp)
REVERT: B  474 MET cc_start: -0.1853 (mmp) cc_final: -0.2686 (mmt)
REVERT: B  572 ASN cc_start: 0.8895 (m-40) cc_final: 0.8631 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 33
  average time/residue: 0.1601
  time to fit residues: 8.3865
Evaluate side-chains
  34 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 23
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  271 TRP
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 14 optimal weight:   30.0000
   chunk 32 optimal weight:   20.0000
   chunk 9 optimal weight:   30.0000
   chunk 21 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.045208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.037549 restraints weight = 92327.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.038341 restraints weight = 54614.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.038849 restraints weight = 36506.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.8772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6701  Z= 0.274
  Angle     :  0.686  10.903   9109  Z= 0.358
  Chirality :  0.045   0.305    965
  Planarity :  0.005   0.046   1171
  Dihedral  :  5.843  39.914    984
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 23.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.52 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.30), residues: 787
  helix: -0.03 (0.25), residues: 407
  sheet:  0.85 (0.73), residues: 45
  loop : -0.69 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 275 
 HIS   0.009   0.002   HIS B 535 
 PHE   0.017   0.002   PHE B 400 
 TYR   0.015   0.002   TYR B 516 
 ARG   0.006   0.001   ARG A 494 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2641.15 seconds
wall clock time: 46 minutes 36.97 seconds (2796.97 seconds total)