Starting phenix.real_space_refine
on Wed Sep 17 19:53:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xvy_38723/09_2025/8xvy_38723.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xvy_38723/09_2025/8xvy_38723.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xvy_38723/09_2025/8xvy_38723.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xvy_38723/09_2025/8xvy_38723.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xvy_38723/09_2025/8xvy_38723.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xvy_38723/09_2025/8xvy_38723.cif"
  }
  resolution = 3.71
  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=   0.008 sd=   0.059
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      39      5.16       5
     C    7254      2.51       5
     N    1737      2.21       5
     O    1893      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  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: 10923
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 5512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 687, 5512
          Classifications: {'peptide': 687}
          Link IDs: {'PTRANS': 31, 'TRANS': 655}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 5411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5411
          Classifications: {'peptide': 674}
          Link IDs: {'PTRANS': 30, 'TRANS': 643}
          Chain breaks: 2
  Time building chain proxies: 2.68, per 1000 atoms: 0.25
  Number of scatterers: 10923
  At special positions: 0
  Unit cell: (86.51, 142.425, 102.335, 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      39     16.00
     O    1893      8.00
     N    1737      7.00
     C    7254      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 419.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2602

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 3 sheets defined
      70.4% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 28
    Processing helix  chain 'B' and resid 29 through 32
      removed outlier: 6.710A  pdb=" N   GLY B  32 " --> pdb=" O   ARG B  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 32'
    Processing helix  chain 'B' and resid 33 through 38
    Processing helix  chain 'B' and resid 56 through 60
    Processing helix  chain 'B' and resid 61 through 67
      removed outlier: 3.722A  pdb=" N   THR B  67 " --> pdb=" O   ARG B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 77
    Processing helix  chain 'B' and resid 78 through 113
      removed outlier: 3.900A  pdb=" N   ALA B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL B  83 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      Proline residue:  B 104  - end of helix
      Proline residue:  B 108  - end of helix
    Processing helix  chain 'B' and resid 132 through 137
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 3.671A  pdb=" N   ASN B 141 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 183
      removed outlier: 3.778A  pdb=" N   ALA B 151 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 191
    Processing helix  chain 'B' and resid 207 through 213
    Processing helix  chain 'B' and resid 215 through 220
    Processing helix  chain 'B' and resid 233 through 261
    Processing helix  chain 'B' and resid 280 through 304
      removed outlier: 4.052A  pdb=" N   ALA B 304 " --> pdb=" O   LYS B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 327
      removed outlier: 3.855A  pdb=" N   ALA B 325 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLN B 326 " --> pdb=" O   ALA B 322 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   SER B 327 " --> pdb=" O   SER B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 389
      Proline residue:  B 380  - end of helix
      removed outlier: 3.917A  pdb=" N   THR B 389 " --> pdb=" O   SER B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 396
      removed outlier: 3.843A  pdb=" N   ARG B 395 " --> pdb=" O   LYS B 391 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE B 396 " --> pdb=" O   ASN B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 401
    Processing helix  chain 'B' and resid 406 through 439
      removed outlier: 3.867A  pdb=" N   ARG B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      Proline residue:  B 418  - end of helix
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 444 through 476
    Processing helix  chain 'B' and resid 477 through 481
      removed outlier: 3.672A  pdb=" N   ILE B 481 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 523
      removed outlier: 3.618A  pdb=" N   ILE B 490 " --> pdb=" O   LYS B 486 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE B 491 " --> pdb=" O   LEU B 487 " (cutoff:3.500A)
      Proline residue:  B 499  - end of helix
    Processing helix  chain 'B' and resid 523 through 530
    Processing helix  chain 'B' and resid 543 through 547
      removed outlier: 3.657A  pdb=" N   GLU B 546 " --> pdb=" O   GLU B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 572
      removed outlier: 3.593A  pdb=" N   VAL B 559 " --> pdb=" O   TYR B 555 " (cutoff:3.500A)
      Proline residue:  B 560  - end of helix
    Processing helix  chain 'B' and resid 578 through 601
      removed outlier: 3.693A  pdb=" N   PHE B 582 " --> pdb=" O   LEU B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 635
      removed outlier: 3.520A  pdb=" N   ILE B 616 " --> pdb=" O   MET B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 645
    Processing helix  chain 'B' and resid 646 through 664
    Processing helix  chain 'B' and resid 665 through 668
    Processing helix  chain 'A' and resid 2 through 29
      removed outlier: 3.624A  pdb=" N   ARG A  29 " --> pdb=" O   THR A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 32
      No H-bonds generated for 'chain 'A' and resid 30 through 32'
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 61 through 67
      removed outlier: 4.085A  pdb=" N   ALA A  65 " --> pdb=" O   TRP A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 78 through 113
      removed outlier: 3.828A  pdb=" N   ALA A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
      Proline residue:  A 104  - end of helix
      Proline residue:  A 108  - end of helix
      removed outlier: 3.700A  pdb=" N   ASP A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 147 through 185
      removed outlier: 3.973A  pdb=" N   ALA A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 191
    Processing helix  chain 'A' and resid 207 through 213
    Processing helix  chain 'A' and resid 215 through 220
    Processing helix  chain 'A' and resid 233 through 261
    Processing helix  chain 'A' and resid 279 through 303
      removed outlier: 3.570A  pdb=" N   LEU A 303 " --> pdb=" O   GLN A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 355 through 388
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 388 through 394
      removed outlier: 3.756A  pdb=" N   GLN A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 438
      removed outlier: 3.651A  pdb=" N   ARG A 410 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      Proline residue:  A 418  - end of helix
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 439 through 441
      No H-bonds generated for 'chain 'A' and resid 439 through 441'
    Processing helix  chain 'A' and resid 444 through 476
    Processing helix  chain 'A' and resid 491 through 523
      removed outlier: 3.970A  pdb=" N   ALA A 495 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   SER A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      Proline residue:  A 499  - end of helix
      removed outlier: 3.886A  pdb=" N   THR A 503 " --> pdb=" O   PRO A 499 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE A 504 " --> pdb=" O   LYS A 500 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A 510 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY A 516 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   TYR A 517 " --> pdb=" O   PHE A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 530
    Processing helix  chain 'A' and resid 543 through 548
    Processing helix  chain 'A' and resid 554 through 572
      Proline residue:  A 560  - end of helix
    Processing helix  chain 'A' and resid 578 through 601
      removed outlier: 3.860A  pdb=" N   PHE A 582 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 638
      removed outlier: 3.772A  pdb=" N   ILE A 616 " --> pdb=" O   MET A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 644
      No H-bonds generated for 'chain 'A' and resid 642 through 644'
    Processing helix  chain 'A' and resid 645 through 665
      removed outlier: 4.023A  pdb=" N   LEU A 649 " --> pdb=" O   LEU A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 669
      removed outlier: 3.531A  pdb=" N   GLU A 669 " --> pdb=" O   GLY A 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 666 through 669'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 229
      removed outlier: 3.561A  pdb=" N   ARG B 226 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   THR B 339 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 268
    Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 231
      removed outlier: 3.613A  pdb=" N   ARG A 226 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ALA A 310 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR A 339 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)

    679 hydrogen bonds defined for protein.
    1986 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: 1.64

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1906
        1.33 -     1.45: 2920
        1.45 -     1.57: 6321
        1.57 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 11211
  Sorted by residual:
  bond pdb=" C   GLU B 619 "
       pdb=" N   ILE B 620 "
    ideal  model  delta    sigma   weight residual
    1.335  1.306  0.029 1.23e-02 6.61e+03 5.69e+00
  bond pdb=" C   GLU B 611 "
       pdb=" O   GLU B 611 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.029 1.31e-02 5.83e+03 5.00e+00
  bond pdb=" CA  GLU B 611 "
       pdb=" C   GLU B 611 "
    ideal  model  delta    sigma   weight residual
    1.522  1.498  0.024 1.37e-02 5.33e+03 3.19e+00
  bond pdb=" N   GLU A 619 "
       pdb=" CA  GLU A 619 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.021 1.17e-02 7.31e+03 3.18e+00
  bond pdb=" C   ILE A 397 "
       pdb=" N   PRO A 398 "
    ideal  model  delta    sigma   weight residual
    1.331  1.353 -0.023 1.31e-02 5.83e+03 3.04e+00
  ... (remaining 11206 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 14665
        1.81 -     3.62: 459
        3.62 -     5.43: 91
        5.43 -     7.24: 17
        7.24 -     9.04: 8
  Bond angle restraints: 15240
  Sorted by residual:
  angle pdb=" N   THR A  55 "
        pdb=" CA  THR A  55 "
        pdb=" C   THR A  55 "
      ideal   model   delta    sigma   weight residual
     114.75  106.02    8.73 1.26e+00 6.30e-01 4.80e+01
  angle pdb=" C   LEU B 626 "
        pdb=" N   PHE B 627 "
        pdb=" CA  PHE B 627 "
      ideal   model   delta    sigma   weight residual
     122.26  115.00    7.26 1.59e+00 3.96e-01 2.08e+01
  angle pdb=" CA  THR A  55 "
        pdb=" C   THR A  55 "
        pdb=" N   ARG A  56 "
      ideal   model   delta    sigma   weight residual
     119.80  114.26    5.54 1.34e+00 5.57e-01 1.71e+01
  angle pdb=" C   VAL A 646 "
        pdb=" N   ILE A 647 "
        pdb=" CA  ILE A 647 "
      ideal   model   delta    sigma   weight residual
     120.24  122.78   -2.54 6.30e-01 2.52e+00 1.62e+01
  angle pdb=" N   TYR A 377 "
        pdb=" CA  TYR A 377 "
        pdb=" C   TYR A 377 "
      ideal   model   delta    sigma   weight residual
     111.24  106.07    5.17 1.29e+00 6.01e-01 1.60e+01
  ... (remaining 15235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5960
       17.94 -    35.87: 532
       35.87 -    53.81: 89
       53.81 -    71.74: 17
       71.74 -    89.68: 8
  Dihedral angle restraints: 6606
    sinusoidal: 2586
      harmonic: 4020
  Sorted by residual:
  dihedral pdb=" CA  PHE B 627 "
           pdb=" C   PHE B 627 "
           pdb=" N   GLN B 628 "
           pdb=" CA  GLN B 628 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.76   30.24     0      5.00e+00 4.00e-02 3.66e+01
  dihedral pdb=" CA  ILE B  42 "
           pdb=" C   ILE B  42 "
           pdb=" N   LEU B  43 "
           pdb=" CA  LEU B  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.02   27.98     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  ILE A  42 "
           pdb=" C   ILE A  42 "
           pdb=" N   LEU A  43 "
           pdb=" CA  LEU A  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.34   26.66     0      5.00e+00 4.00e-02 2.84e+01
  ... (remaining 6603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1264
       0.044 -    0.088: 388
       0.088 -    0.131: 96
       0.131 -    0.175: 14
       0.175 -    0.219: 5
  Chirality restraints: 1767
  Sorted by residual:
  chirality pdb=" CA  PHE B 627 "
            pdb=" N   PHE B 627 "
            pdb=" C   PHE B 627 "
            pdb=" CB  PHE B 627 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  ILE A 381 "
            pdb=" CA  ILE A 381 "
            pdb=" CG1 ILE A 381 "
            pdb=" CG2 ILE A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CG  LEU B 624 "
            pdb=" CB  LEU B 624 "
            pdb=" CD1 LEU B 624 "
            pdb=" CD2 LEU B 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1764 not shown)

  Planarity restraints: 1864
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 171 "    0.025 2.00e-02 2.50e+03   2.13e-02 9.12e+00
        pdb=" CG  TYR B 171 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 171 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 171 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 171 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 171 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 171 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 171 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  47 "   -0.048 5.00e-02 4.00e+02   7.42e-02 8.80e+00
        pdb=" N   PRO A  48 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A  48 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  48 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 610 "    0.015 2.00e-02 2.50e+03   2.91e-02 8.47e+00
        pdb=" C   GLY B 610 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLY B 610 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLU B 611 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1861 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 229
        2.68 -     3.24: 11755
        3.24 -     3.79: 17465
        3.79 -     4.35: 22451
        4.35 -     4.90: 36106
  Nonbonded interactions: 88006
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  80 "
            pdb=" OG  SER B 608 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OH  TYR B 215 "
            pdb=" OE2 GLU A 674 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" O   PHE A 504 "
            pdb=" OG1 THR A 507 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OD2 ASP A  80 "
            pdb=" OG  SER A 608 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" OE2 GLU B 674 "
            pdb=" OH  TYR A 215 "
     model   vdw
     2.193 3.040
  ... (remaining 88001 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 1 through 476 or resid 490 through 696))
}

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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.940
  Find NCS groups from input model:        0.130
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11211  Z= 0.205
  Angle     :  0.805   9.044  15240  Z= 0.470
  Chirality :  0.045   0.219   1767
  Planarity :  0.005   0.074   1864
  Dihedral  : 14.036  89.679   4004
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.59 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 (0.23), residues: 1351
  helix:  0.59 (0.18), residues: 873
  sheet: -3.24 (0.94), residues: 32
  loop : -2.07 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 252 
 TYR   0.053   0.002   TYR B 171 
 PHE   0.036   0.002   PHE B 513 
 TRP   0.025   0.002   TRP A 613 
 HIS   0.006   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (11211)
  covalent geometry    : angle       0.80542 (15240)
  hydrogen bonds       : bond        0.13718 (  679)
  hydrogen bonds       : angle       6.16915 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 235
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: B   27 LEU cc_start: 0.8908 (tp) cc_final: 0.8529 (tp)
REVERT: B  198 ASP cc_start: 0.7995 (t0) cc_final: 0.7596 (t0)
REVERT: B  378 MET cc_start: 0.8484 (tpt) cc_final: 0.8173 (tpp)
REVERT: B  437 SER cc_start: 0.9426 (t) cc_final: 0.9174 (t)
REVERT: B  522 SER cc_start: 0.9417 (p) cc_final: 0.9213 (p)
REVERT: B  658 TYR cc_start: 0.8388 (t80) cc_final: 0.8055 (t80)
REVERT: A    1 MET cc_start: 0.6490 (mmp) cc_final: 0.5745 (ttt)
REVERT: A  250 LEU cc_start: 0.9356 (tt) cc_final: 0.8927 (pp)
REVERT: A  308 GLN cc_start: 0.8058 (mm110) cc_final: 0.7591 (mm-40)
REVERT: A  459 PHE cc_start: 0.7970 (t80) cc_final: 0.7678 (t80)
REVERT: A  571 CYS cc_start: 0.9270 (t) cc_final: 0.8994 (t)
REVERT: A  619 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5700 (mp0)
  outliers start: 2
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0768
  time to fit residues: 28.2816
Evaluate side-chains
  182 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  619 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:   50.0000
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 463 ASN
B 615 HIS
** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
A 447 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.149131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.105912 restraints weight = 20347.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109488 restraints weight = 10253.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.111690 restraints weight = 7056.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.112716 restraints weight = 5768.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.113543 restraints weight = 5235.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11211  Z= 0.202
  Angle     :  0.736  13.526  15240  Z= 0.380
  Chirality :  0.046   0.220   1767
  Planarity :  0.005   0.061   1864
  Dihedral  :  5.905  59.929   1469
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.73 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.23), residues: 1351
  helix:  0.65 (0.18), residues: 887
  sheet: -3.03 (1.32), residues: 17
  loop : -1.81 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 558 
 TYR   0.043   0.002   TYR A 377 
 PHE   0.047   0.002   PHE B 627 
 TRP   0.024   0.001   TRP A 613 
 HIS   0.005   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (11211)
  covalent geometry    : angle       0.73650 (15240)
  hydrogen bonds       : bond        0.05285 (  679)
  hydrogen bonds       : angle       5.19539 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 206
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: B    3 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6425 (m-10)
REVERT: B   27 LEU cc_start: 0.8979 (tp) cc_final: 0.8682 (tp)
REVERT: B  198 ASP cc_start: 0.7814 (t0) cc_final: 0.7186 (t70)
REVERT: B  378 MET cc_start: 0.8637 (tpt) cc_final: 0.8263 (tpp)
REVERT: B  463 ASN cc_start: 0.7683 (m-40) cc_final: 0.7482 (t0)
REVERT: B  563 MET cc_start: 0.9035 (mmm) cc_final: 0.8730 (mmm)
REVERT: A  100 LEU cc_start: 0.8583 (mt) cc_final: 0.8283 (mp)
REVERT: A  139 MET cc_start: 0.8080 (ttm) cc_final: 0.7151 (ttm)
REVERT: A  198 ASP cc_start: 0.8252 (m-30) cc_final: 0.7953 (m-30)
REVERT: A  250 LEU cc_start: 0.9308 (tt) cc_final: 0.8959 (pp)
REVERT: A  308 GLN cc_start: 0.8050 (mm110) cc_final: 0.7384 (mm-40)
REVERT: A  571 CYS cc_start: 0.9241 (t) cc_final: 0.8939 (t)
REVERT: A  669 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8129 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 212
  average time/residue: 0.0725
  time to fit residues: 24.1260
Evaluate side-chains
  186 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  619 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 123 optimal weight:    0.9980
   chunk 92 optimal weight:    7.9990
   chunk 110 optimal weight:    0.9980
   chunk 133 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 125 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B 266 ASN
B 628 GLN
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.149783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.109058 restraints weight = 20384.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.112496 restraints weight = 10145.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112884 restraints weight = 6896.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.113730 restraints weight = 6269.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.113698 restraints weight = 5729.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11211  Z= 0.171
  Angle     :  0.698  12.930  15240  Z= 0.356
  Chirality :  0.045   0.217   1767
  Planarity :  0.005   0.054   1864
  Dihedral  :  5.772  59.620   1469
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.79 %
    Favored  : 83.76 %
  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: -0.16 (0.24), residues: 1351
  helix:  0.75 (0.18), residues: 890
  sheet: -3.72 (1.71), residues: 10
  loop : -1.73 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.023   0.002   TYR B 171 
 PHE   0.047   0.002   PHE B 627 
 TRP   0.021   0.001   TRP A 613 
 HIS   0.004   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (11211)
  covalent geometry    : angle       0.69828 (15240)
  hydrogen bonds       : bond        0.04959 (  679)
  hydrogen bonds       : angle       4.96365 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.6351 (m-80)
REVERT: B  171 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8998 (t80)
REVERT: B  198 ASP cc_start: 0.7886 (t0) cc_final: 0.7163 (t70)
REVERT: B  463 ASN cc_start: 0.7350 (m-40) cc_final: 0.6881 (t0)
REVERT: B  563 MET cc_start: 0.9085 (mmm) cc_final: 0.8832 (mmm)
REVERT: A  100 LEU cc_start: 0.8577 (mt) cc_final: 0.8243 (mp)
REVERT: A  198 ASP cc_start: 0.8357 (m-30) cc_final: 0.8019 (m-30)
REVERT: A  250 LEU cc_start: 0.9325 (tt) cc_final: 0.8990 (pp)
REVERT: A  571 CYS cc_start: 0.9191 (t) cc_final: 0.8911 (t)
REVERT: A  669 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8045 (mt-10)
  outliers start: 29
  outliers final: 18
  residues processed: 229
  average time/residue: 0.0679
  time to fit residues: 24.7047
Evaluate side-chains
  215 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  462 PHE
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  619 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    8.9990
   chunk 107 optimal weight:   40.0000
   chunk 108 optimal weight:   10.0000
   chunk 132 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.147139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.104702 restraints weight = 20345.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.108216 restraints weight = 10395.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110392 restraints weight = 7171.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.111638 restraints weight = 5871.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.112092 restraints weight = 5283.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11211  Z= 0.184
  Angle     :  0.695  11.188  15240  Z= 0.356
  Chirality :  0.044   0.215   1767
  Planarity :  0.005   0.050   1864
  Dihedral  :  5.695  59.950   1469
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.10 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.16 %
    Favored  : 81.05 %
  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: -0.02 (0.24), residues: 1351
  helix:  0.87 (0.18), residues: 891
  sheet: -3.45 (1.76), residues: 10
  loop : -1.73 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 252 
 TYR   0.041   0.002   TYR A 171 
 PHE   0.045   0.002   PHE B 627 
 TRP   0.018   0.001   TRP A 613 
 HIS   0.003   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (11211)
  covalent geometry    : angle       0.69520 (15240)
  hydrogen bonds       : bond        0.04830 (  679)
  hydrogen bonds       : angle       4.84599 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 203
  time to evaluate  : 0.312 
Fit side-chains
REVERT: B   49 TRP cc_start: 0.7607 (p90) cc_final: 0.7365 (p90)
REVERT: B  171 TYR cc_start: 0.9290 (OUTLIER) cc_final: 0.9021 (t80)
REVERT: B  198 ASP cc_start: 0.7930 (t0) cc_final: 0.7161 (t70)
REVERT: B  489 MET cc_start: 0.8686 (ppp) cc_final: 0.8450 (ppp)
REVERT: B  563 MET cc_start: 0.9169 (mmm) cc_final: 0.8760 (mmm)
REVERT: A   21 MET cc_start: 0.9491 (mmm) cc_final: 0.9273 (mmm)
REVERT: A  100 LEU cc_start: 0.8616 (mt) cc_final: 0.8269 (mp)
REVERT: A  139 MET cc_start: 0.6777 (ttp) cc_final: 0.5916 (ttm)
REVERT: A  250 LEU cc_start: 0.9297 (tt) cc_final: 0.8980 (pp)
REVERT: A  571 CYS cc_start: 0.9215 (t) cc_final: 0.8945 (t)
REVERT: A  669 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8043 (mt-10)
  outliers start: 33
  outliers final: 25
  residues processed: 222
  average time/residue: 0.0729
  time to fit residues: 25.3434
Evaluate side-chains
  215 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  399 PHE
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  506 LEU
Chi-restraints excluded: chain B residue  519 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain B residue  691 ARG
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  462 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  653 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 119 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B  33 ASN
B 531 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.147714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.105031 restraints weight = 20140.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.108597 restraints weight = 10272.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.110731 restraints weight = 7073.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.112028 restraints weight = 5814.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.112369 restraints weight = 5223.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11211  Z= 0.166
  Angle     :  0.679  11.368  15240  Z= 0.347
  Chirality :  0.044   0.229   1767
  Planarity :  0.005   0.051   1864
  Dihedral  :  5.600  59.331   1469
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.16 %
    Favored  : 80.63 %
  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:  0.09 (0.24), residues: 1351
  helix:  0.96 (0.18), residues: 894
  sheet: -2.39 (1.30), residues: 20
  loop : -1.70 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 410 
 TYR   0.027   0.002   TYR A 171 
 PHE   0.046   0.002   PHE B 627 
 TRP   0.020   0.001   TRP A 613 
 HIS   0.002   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11211)
  covalent geometry    : angle       0.67910 (15240)
  hydrogen bonds       : bond        0.04659 (  679)
  hydrogen bonds       : angle       4.74065 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 204
  time to evaluate  : 0.404 
Fit side-chains
REVERT: B   49 TRP cc_start: 0.7681 (p90) cc_final: 0.7445 (p90)
REVERT: B  171 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.9035 (t80)
REVERT: B  198 ASP cc_start: 0.7889 (t0) cc_final: 0.7097 (t70)
REVERT: B  357 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6898 (m-10)
REVERT: B  563 MET cc_start: 0.9115 (mmm) cc_final: 0.8419 (mmm)
REVERT: B  594 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9029 (tt)
REVERT: A   21 MET cc_start: 0.9510 (mmm) cc_final: 0.9257 (mmm)
REVERT: A  250 LEU cc_start: 0.9275 (tt) cc_final: 0.8992 (pp)
REVERT: A  364 TYR cc_start: 0.8119 (m-80) cc_final: 0.7821 (m-80)
REVERT: A  440 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7691 (mt-10)
REVERT: A  571 CYS cc_start: 0.9155 (t) cc_final: 0.8878 (t)
REVERT: A  669 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8038 (mt-10)
  outliers start: 38
  outliers final: 26
  residues processed: 226
  average time/residue: 0.0716
  time to fit residues: 25.2845
Evaluate side-chains
  217 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  399 PHE
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  462 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  653 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0270
   chunk 1 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.149733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107822 restraints weight = 20145.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.111342 restraints weight = 10272.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.113582 restraints weight = 7074.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.114716 restraints weight = 5777.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.115502 restraints weight = 5217.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11211  Z= 0.142
  Angle     :  0.687  14.523  15240  Z= 0.346
  Chirality :  0.044   0.233   1767
  Planarity :  0.004   0.050   1864
  Dihedral  :  5.516  59.302   1469
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.85 %
    Favored  : 78.85 %
  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:  0.27 (0.24), residues: 1351
  helix:  1.16 (0.18), residues: 874
  sheet: -2.14 (1.29), residues: 20
  loop : -1.66 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 148 
 TYR   0.043   0.002   TYR A 171 
 PHE   0.060   0.002   PHE B 627 
 TRP   0.018   0.001   TRP A 613 
 HIS   0.002   0.000   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11211)
  covalent geometry    : angle       0.68695 (15240)
  hydrogen bonds       : bond        0.04570 (  679)
  hydrogen bonds       : angle       4.69754 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 204
  time to evaluate  : 0.404 
Fit side-chains
REVERT: B   49 TRP cc_start: 0.7564 (p90) cc_final: 0.7332 (p90)
REVERT: B  171 TYR cc_start: 0.9256 (OUTLIER) cc_final: 0.9010 (t80)
REVERT: B  198 ASP cc_start: 0.7794 (t0) cc_final: 0.6959 (t70)
REVERT: B  357 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6806 (m-10)
REVERT: B  489 MET cc_start: 0.8491 (ppp) cc_final: 0.8214 (ppp)
REVERT: B  594 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8999 (tt)
REVERT: B  631 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8610 (tpp)
REVERT: A  250 LEU cc_start: 0.9267 (tt) cc_final: 0.8980 (pp)
REVERT: A  332 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7861 (mpp)
REVERT: A  364 TYR cc_start: 0.8055 (m-80) cc_final: 0.7778 (m-80)
REVERT: A  440 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: A  571 CYS cc_start: 0.9154 (t) cc_final: 0.8880 (t)
REVERT: A  669 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8062 (mt-10)
  outliers start: 39
  outliers final: 21
  residues processed: 224
  average time/residue: 0.0780
  time to fit residues: 27.2113
Evaluate side-chains
  209 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  399 PHE
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  631 MET
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain B residue  691 ARG
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  619 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 131 optimal weight:    0.8980
   chunk 113 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 106 optimal weight:    8.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.149362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.106955 restraints weight = 20213.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110530 restraints weight = 10340.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.112708 restraints weight = 7118.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.113831 restraints weight = 5844.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.114423 restraints weight = 5273.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11211  Z= 0.155
  Angle     :  0.710  13.939  15240  Z= 0.355
  Chirality :  0.045   0.373   1767
  Planarity :  0.004   0.050   1864
  Dihedral  :  5.447  59.184   1469
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.04 %
    Favored  : 77.58 %
  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:  0.27 (0.24), residues: 1351
  helix:  1.15 (0.18), residues: 879
  sheet: -2.04 (1.25), residues: 20
  loop : -1.66 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 410 
 TYR   0.027   0.002   TYR A 171 
 PHE   0.072   0.002   PHE B 627 
 TRP   0.020   0.001   TRP A 613 
 HIS   0.005   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (11211)
  covalent geometry    : angle       0.70975 (15240)
  hydrogen bonds       : bond        0.04553 (  679)
  hydrogen bonds       : angle       4.67025 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 194
  time to evaluate  : 0.434 
Fit side-chains
REVERT: B    1 MET cc_start: 0.8948 (mpp) cc_final: 0.8472 (mpp)
REVERT: B   49 TRP cc_start: 0.7604 (p90) cc_final: 0.7372 (p90)
REVERT: B   56 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6760 (mtp180)
REVERT: B  171 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.8954 (t80)
REVERT: B  198 ASP cc_start: 0.7797 (t0) cc_final: 0.6970 (t70)
REVERT: B  332 MET cc_start: 0.7267 (mtp) cc_final: 0.6813 (mpp)
REVERT: B  357 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6691 (m-10)
REVERT: B  414 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8321 (pt0)
REVERT: B  489 MET cc_start: 0.8575 (ppp) cc_final: 0.8357 (ppp)
REVERT: B  594 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8954 (tt)
REVERT: B  631 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8581 (tpp)
REVERT: A   21 MET cc_start: 0.9476 (mmm) cc_final: 0.9196 (mmm)
REVERT: A  250 LEU cc_start: 0.9280 (tt) cc_final: 0.8989 (pp)
REVERT: A  332 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7849 (mpp)
REVERT: A  364 TYR cc_start: 0.8070 (m-80) cc_final: 0.7754 (m-80)
REVERT: A  440 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: A  571 CYS cc_start: 0.9150 (t) cc_final: 0.8839 (t)
REVERT: A  627 PHE cc_start: 0.6295 (m-80) cc_final: 0.6042 (m-80)
REVERT: A  669 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8066 (mt-10)
  outliers start: 40
  outliers final: 24
  residues processed: 217
  average time/residue: 0.0789
  time to fit residues: 26.7210
Evaluate side-chains
  215 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  399 PHE
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  631 MET
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  462 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  653 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 121 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   chunk 98 optimal weight:    0.9990
   chunk 122 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 392 ASN
** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 628 GLN
A 206 GLN
A 447 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.149917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107892 restraints weight = 20220.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.111498 restraints weight = 10247.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.113735 restraints weight = 7012.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.114535 restraints weight = 5710.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.115341 restraints weight = 5220.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11211  Z= 0.150
  Angle     :  0.696  11.621  15240  Z= 0.350
  Chirality :  0.044   0.222   1767
  Planarity :  0.004   0.047   1864
  Dihedral  :  5.380  59.021   1469
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.80 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1351
  helix:  1.22 (0.18), residues: 876
  sheet: -1.95 (1.23), residues: 20
  loop : -1.69 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 410 
 TYR   0.024   0.001   TYR B 171 
 PHE   0.066   0.002   PHE B 627 
 TRP   0.021   0.001   TRP A  49 
 HIS   0.005   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11211)
  covalent geometry    : angle       0.69584 (15240)
  hydrogen bonds       : bond        0.04512 (  679)
  hydrogen bonds       : angle       4.63644 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 194
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.8989 (mpp) cc_final: 0.8567 (mpp)
REVERT: B   49 TRP cc_start: 0.7670 (p90) cc_final: 0.7447 (p90)
REVERT: B   56 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6751 (mtp180)
REVERT: B  171 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.8965 (t80)
REVERT: B  198 ASP cc_start: 0.7777 (t0) cc_final: 0.6918 (t70)
REVERT: B  332 MET cc_start: 0.7228 (mtp) cc_final: 0.6800 (mpp)
REVERT: B  357 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6685 (m-10)
REVERT: B  395 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8228 (ptt180)
REVERT: B  414 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8324 (pt0)
REVERT: B  489 MET cc_start: 0.8589 (ppp) cc_final: 0.8381 (ppp)
REVERT: B  594 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8965 (tt)
REVERT: B  631 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8598 (tpp)
REVERT: B  691 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7725 (ptp-110)
REVERT: A   21 MET cc_start: 0.9480 (mmm) cc_final: 0.9172 (mmm)
REVERT: A  250 LEU cc_start: 0.9279 (tt) cc_final: 0.9028 (pp)
REVERT: A  332 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7871 (mpp)
REVERT: A  364 TYR cc_start: 0.8037 (m-80) cc_final: 0.7729 (m-80)
REVERT: A  440 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7567 (mt-10)
REVERT: A  571 CYS cc_start: 0.9135 (t) cc_final: 0.8841 (t)
REVERT: A  669 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8013 (mt-10)
  outliers start: 40
  outliers final: 25
  residues processed: 213
  average time/residue: 0.0769
  time to fit residues: 25.5714
Evaluate side-chains
  217 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 185
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  399 PHE
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  538 CYS
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  631 MET
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain B residue  691 ARG
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  462 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  653 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 56 optimal weight:    0.0170
   chunk 96 optimal weight:    0.9980
   chunk 125 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 128 optimal weight:    2.9990
   chunk 46 optimal weight:    0.2980
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 492 ASN
A 447 HIS

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 = 0.151762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.109413 restraints weight = 20121.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113059 restraints weight = 10299.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.115331 restraints weight = 7065.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.116605 restraints weight = 5760.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.117025 restraints weight = 5176.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11211  Z= 0.142
  Angle     :  0.702  15.460  15240  Z= 0.348
  Chirality :  0.044   0.215   1767
  Planarity :  0.004   0.044   1864
  Dihedral  :  5.301  58.748   1469
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.47 %
    Favored  : 76.31 %
  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:  0.35 (0.24), residues: 1351
  helix:  1.20 (0.18), residues: 880
  sheet: -1.89 (1.22), residues: 20
  loop : -1.61 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 410 
 TYR   0.023   0.001   TYR B 171 
 PHE   0.054   0.002   PHE B 627 
 TRP   0.018   0.001   TRP A 613 
 HIS   0.005   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11211)
  covalent geometry    : angle       0.70222 (15240)
  hydrogen bonds       : bond        0.04423 (  679)
  hydrogen bonds       : angle       4.64642 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 193
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.9092 (mpp) cc_final: 0.8698 (mpp)
REVERT: B   49 TRP cc_start: 0.7626 (p90) cc_final: 0.7382 (p90)
REVERT: B   56 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6698 (mtp180)
REVERT: B  171 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.9036 (t80)
REVERT: B  198 ASP cc_start: 0.7643 (t0) cc_final: 0.6804 (t70)
REVERT: B  240 TRP cc_start: 0.9009 (t60) cc_final: 0.8709 (t60)
REVERT: B  279 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8459 (t0)
REVERT: B  332 MET cc_start: 0.7148 (mtp) cc_final: 0.6744 (mpp)
REVERT: B  357 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6531 (m-10)
REVERT: B  395 ARG cc_start: 0.8435 (ptm160) cc_final: 0.8189 (ptt180)
REVERT: B  463 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7013 (t0)
REVERT: B  489 MET cc_start: 0.8575 (ppp) cc_final: 0.8295 (ppp)
REVERT: B  594 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8945 (tt)
REVERT: B  631 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8657 (tpp)
REVERT: B  691 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7696 (ptp-110)
REVERT: A   21 MET cc_start: 0.9467 (mmm) cc_final: 0.9188 (mmm)
REVERT: A  250 LEU cc_start: 0.9306 (tt) cc_final: 0.8975 (pp)
REVERT: A  332 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7838 (mpp)
REVERT: A  364 TYR cc_start: 0.7980 (m-80) cc_final: 0.7727 (m-80)
REVERT: A  440 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7571 (mt-10)
REVERT: A  571 CYS cc_start: 0.9078 (t) cc_final: 0.8769 (t)
REVERT: A  627 PHE cc_start: 0.6186 (m-80) cc_final: 0.5961 (m-80)
REVERT: A  669 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7990 (mt-10)
  outliers start: 38
  outliers final: 23
  residues processed: 215
  average time/residue: 0.0751
  time to fit residues: 24.7116
Evaluate side-chains
  222 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  399 PHE
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  538 CYS
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  631 MET
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain B residue  691 ARG
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  462 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  619 GLU
Chi-restraints excluded: chain A residue  653 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0370
   chunk 29 optimal weight:    0.0020
   chunk 88 optimal weight:    0.8980
   chunk 51 optimal weight:    0.2980
   chunk 74 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 56 optimal weight:    0.4980
   overall best weight:    0.3466

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

Flipped N/Q/H residues before XYZ refinement:
** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.153529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111330 restraints weight = 20150.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.115025 restraints weight = 10330.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117328 restraints weight = 7089.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.118172 restraints weight = 5773.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.119255 restraints weight = 5268.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11211  Z= 0.139
  Angle     :  0.715  15.818  15240  Z= 0.354
  Chirality :  0.044   0.213   1767
  Planarity :  0.004   0.044   1864
  Dihedral  :  5.255  58.708   1469
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.66 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.24), residues: 1351
  helix:  1.19 (0.18), residues: 875
  sheet: -1.83 (1.20), residues: 20
  loop : -1.59 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  63 
 TYR   0.028   0.001   TYR B 225 
 PHE   0.048   0.002   PHE B 627 
 TRP   0.018   0.001   TRP A 613 
 HIS   0.006   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11211)
  covalent geometry    : angle       0.71479 (15240)
  hydrogen bonds       : bond        0.04367 (  679)
  hydrogen bonds       : angle       4.65173 ( 1986)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 201
  time to evaluate  : 0.394 
Fit side-chains
REVERT: B    1 MET cc_start: 0.9116 (mpp) cc_final: 0.8843 (mpp)
REVERT: B   49 TRP cc_start: 0.7629 (p90) cc_final: 0.7362 (p90)
REVERT: B   56 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6647 (mtp180)
REVERT: B  198 ASP cc_start: 0.7557 (t0) cc_final: 0.6627 (t70)
REVERT: B  240 TRP cc_start: 0.9010 (t60) cc_final: 0.8696 (t60)
REVERT: B  279 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8419 (t0)
REVERT: B  332 MET cc_start: 0.7085 (mtp) cc_final: 0.6832 (mpp)
REVERT: B  334 ASP cc_start: 0.7765 (m-30) cc_final: 0.6874 (m-30)
REVERT: B  336 TRP cc_start: 0.8932 (m100) cc_final: 0.7879 (m100)
REVERT: B  357 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6581 (m-10)
REVERT: B  395 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8172 (ptt180)
REVERT: B  413 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9038 (mp)
REVERT: B  463 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.6990 (t0)
REVERT: B  594 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8906 (tt)
REVERT: B  631 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8639 (tpp)
REVERT: B  691 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7691 (ptp-110)
REVERT: A   21 MET cc_start: 0.9455 (mmm) cc_final: 0.9180 (mmm)
REVERT: A  250 LEU cc_start: 0.9307 (tt) cc_final: 0.8985 (pp)
REVERT: A  332 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7777 (mpp)
REVERT: A  364 TYR cc_start: 0.7948 (m-80) cc_final: 0.7679 (m-80)
REVERT: A  440 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7490 (mt-10)
REVERT: A  571 CYS cc_start: 0.9076 (t) cc_final: 0.8785 (t)
REVERT: A  669 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8005 (mt-10)
  outliers start: 31
  outliers final: 18
  residues processed: 219
  average time/residue: 0.0751
  time to fit residues: 25.8190
Evaluate side-chains
  216 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 189
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  279 ASP
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  399 PHE
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  538 CYS
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  631 MET
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  677 CYS
Chi-restraints excluded: chain B residue  691 ARG
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  513 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0040
   chunk 93 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 67 optimal weight:    0.1980
   chunk 112 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
A 447 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.153481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.111211 restraints weight = 20293.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.114925 restraints weight = 10384.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.117228 restraints weight = 7111.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.118147 restraints weight = 5771.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.118934 restraints weight = 5238.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11211  Z= 0.144
  Angle     :  0.726  15.821  15240  Z= 0.359
  Chirality :  0.045   0.190   1767
  Planarity :  0.004   0.044   1864
  Dihedral  :  4.999  25.380   1466
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.42 %
    Favored  : 74.53 %
  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:  0.28 (0.24), residues: 1351
  helix:  1.17 (0.18), residues: 870
  sheet: -1.83 (1.16), residues: 20
  loop : -1.64 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 362 
 TYR   0.027   0.001   TYR B 225 
 PHE   0.046   0.002   PHE B 627 
 TRP   0.016   0.001   TRP A 613 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (11211)
  covalent geometry    : angle       0.72587 (15240)
  hydrogen bonds       : bond        0.04352 (  679)
  hydrogen bonds       : angle       4.64605 ( 1986)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1805.29 seconds
wall clock time: 32 minutes 7.31 seconds (1927.31 seconds total)