Starting phenix.real_space_refine
on Tue Mar  3 23:47:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qpc_4613/03_2026/6qpc_4613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qpc_4613/03_2026/6qpc_4613.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qpc_4613/03_2026/6qpc_4613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qpc_4613/03_2026/6qpc_4613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qpc_4613/03_2026/6qpc_4613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qpc_4613/03_2026/6qpc_4613.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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: 6
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     P       2      5.49       5
     S      62      5.16       5
     C    6040      2.51       5
     N    1454      2.21       5
     O    1578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9140
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 577, 4530
          Classifications: {'peptide': 577}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 28, 'TRANS': 548}
          Chain breaks: 10
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 236
          Unresolved non-hydrogen angles: 299
          Unresolved non-hydrogen dihedrals: 204
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'HIS:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 126
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 40
          Unusual residues: {' CA': 2, 'P1O': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.86, per 1000 atoms: 0.31
  Number of scatterers: 9140
  At special positions: 0
  Unit cell: (94.116, 110.308, 109.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      4     19.99
     S      62     16.00
     P       2     15.00
     O    1578      8.00
     N    1454      7.00
     C    6040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 352 " - pdb=" SG  CYS A 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 338 " - pdb=" SG  CYS B 365 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 349 " - pdb=" SG  CYS B 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 352 " - pdb=" SG  CYS B 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 601 " distance=2.02

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 334.9 milliseconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2200

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 2 sheets defined
      70.3% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 107
      removed outlier: 3.556A  pdb=" N   ARG A  98 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 142
    Processing helix  chain 'A' and resid 205 through 214
    Processing helix  chain 'A' and resid 265 through 273
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 284 through 292
    Processing helix  chain 'A' and resid 293 through 327
      removed outlier: 3.533A  pdb=" N   LEU A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'A' and resid 360 through 363
      removed outlier: 3.914A  pdb=" N   ILE A 363 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 360 through 363'
    Processing helix  chain 'A' and resid 364 through 375
      removed outlier: 4.376A  pdb=" N   LYS A 370 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 404
      removed outlier: 3.620A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 487
      removed outlier: 3.667A  pdb=" N   ILE A 475 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 539
    Processing helix  chain 'A' and resid 543 through 573
      removed outlier: 4.855A  pdb=" N   SER A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   CYS A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 637
      Proline residue:  A 628  - end of helix
    Processing helix  chain 'A' and resid 648 through 655
      removed outlier: 3.656A  pdb=" N   HIS A 655 " --> pdb=" O   GLU A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 680
    Processing helix  chain 'A' and resid 687 through 710
      removed outlier: 3.854A  pdb=" N   LEU A 698 " --> pdb=" O   VAL A 694 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 746
      removed outlier: 3.750A  pdb=" N   ILE A 728 " --> pdb=" O   ALA A 724 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL A 737 " --> pdb=" O   ALA A 733 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 761
      removed outlier: 3.516A  pdb=" N   ARG A 753 " --> pdb=" O   ASP A 749 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   SER A 761 " --> pdb=" O   TYR A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 781
      removed outlier: 3.600A  pdb=" N   ASN A 779 " --> pdb=" O   GLY A 775 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU A 781 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 857
    Processing helix  chain 'B' and resid 95 through 107
    Processing helix  chain 'B' and resid 131 through 142
    Processing helix  chain 'B' and resid 205 through 214
    Processing helix  chain 'B' and resid 265 through 273
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 284 through 292
    Processing helix  chain 'B' and resid 293 through 327
      removed outlier: 3.533A  pdb=" N   LEU B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 330
      No H-bonds generated for 'chain 'B' and resid 328 through 330'
    Processing helix  chain 'B' and resid 331 through 339
    Processing helix  chain 'B' and resid 360 through 363
      removed outlier: 3.914A  pdb=" N   ILE B 363 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 360 through 363'
    Processing helix  chain 'B' and resid 364 through 375
      removed outlier: 4.375A  pdb=" N   LYS B 370 " --> pdb=" O   GLU B 366 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ILE B 373 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 404
      removed outlier: 3.620A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 487
      removed outlier: 3.666A  pdb=" N   ILE B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 539
    Processing helix  chain 'B' and resid 543 through 573
      removed outlier: 4.854A  pdb=" N   SER B 566 " --> pdb=" O   ASN B 562 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   CYS B 567 " --> pdb=" O   TYR B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 637
      Proline residue:  B 628  - end of helix
    Processing helix  chain 'B' and resid 648 through 655
      removed outlier: 3.657A  pdb=" N   HIS B 655 " --> pdb=" O   GLU B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 680
    Processing helix  chain 'B' and resid 687 through 710
      removed outlier: 3.855A  pdb=" N   LEU B 698 " --> pdb=" O   VAL B 694 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG B 701 " --> pdb=" O   ILE B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 746
      removed outlier: 3.751A  pdb=" N   ILE B 728 " --> pdb=" O   ALA B 724 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL B 737 " --> pdb=" O   ALA B 733 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 749 through 761
      removed outlier: 3.516A  pdb=" N   ARG B 753 " --> pdb=" O   ASP B 749 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER B 761 " --> pdb=" O   TYR B 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 781
      removed outlier: 3.601A  pdb=" N   ASN B 779 " --> pdb=" O   GLY B 775 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU B 781 " --> pdb=" O   ILE B 777 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 857
    Processing sheet with id=AA1, first strand: chain 'A' and resid 782 through 783
    Processing sheet with id=AA2, first strand: chain 'B' and resid 782 through 783

    592 hydrogen bonds defined for protein.
    1758 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: 1.39

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1464
        1.32 -     1.45: 2722
        1.45 -     1.58: 5080
        1.58 -     1.71: 6
        1.71 -     1.83: 100
  Bond restraints: 9372
  Sorted by residual:
  bond pdb=" O3  P1O A1003 "
       pdb=" P1  P1O A1003 "
    ideal  model  delta    sigma   weight residual
    1.648  1.770 -0.122 2.00e-02 2.50e+03 3.75e+01
  bond pdb=" O3  P1O B1003 "
       pdb=" P1  P1O B1003 "
    ideal  model  delta    sigma   weight residual
    1.648  1.770 -0.122 2.00e-02 2.50e+03 3.74e+01
  bond pdb=" C19 P1O A1003 "
       pdb=" C20 P1O A1003 "
    ideal  model  delta    sigma   weight residual
    1.502  1.584 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" C19 P1O B1003 "
       pdb=" C20 P1O B1003 "
    ideal  model  delta    sigma   weight residual
    1.502  1.583 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C1  P1O B1003 "
       pdb=" C2  P1O B1003 "
    ideal  model  delta    sigma   weight residual
    1.513  1.589 -0.076 2.00e-02 2.50e+03 1.45e+01
  ... (remaining 9367 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 12234
        2.26 -     4.52: 418
        4.52 -     6.78: 50
        6.78 -     9.04: 26
        9.04 -    11.30: 6
  Bond angle restraints: 12734
  Sorted by residual:
  angle pdb=" CA  TYR A 477 "
        pdb=" CB  TYR A 477 "
        pdb=" CG  TYR A 477 "
      ideal   model   delta    sigma   weight residual
     113.90  122.44   -8.54 1.80e+00 3.09e-01 2.25e+01
  angle pdb=" CA  TYR B 477 "
        pdb=" CB  TYR B 477 "
        pdb=" CG  TYR B 477 "
      ideal   model   delta    sigma   weight residual
     113.90  122.42   -8.52 1.80e+00 3.09e-01 2.24e+01
  angle pdb=" C   LEU B 503 "
        pdb=" N   THR B 504 "
        pdb=" CA  THR B 504 "
      ideal   model   delta    sigma   weight residual
     121.62  128.96   -7.34 1.57e+00 4.06e-01 2.18e+01
  angle pdb=" C   LEU A 503 "
        pdb=" N   THR A 504 "
        pdb=" CA  THR A 504 "
      ideal   model   delta    sigma   weight residual
     121.62  128.94   -7.32 1.57e+00 4.06e-01 2.17e+01
  angle pdb=" C   VAL A 484 "
        pdb=" N   PHE A 485 "
        pdb=" CA  PHE A 485 "
      ideal   model   delta    sigma   weight residual
     120.29  113.76    6.53 1.42e+00 4.96e-01 2.11e+01
  ... (remaining 12729 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.87: 5251
       27.87 -    55.73: 227
       55.73 -    83.60: 18
       83.60 -   111.47: 2
      111.47 -   139.34: 2
  Dihedral angle restraints: 5500
    sinusoidal: 2100
      harmonic: 3400
  Sorted by residual:
  dihedral pdb=" CA  ARG A 354 "
           pdb=" C   ARG A 354 "
           pdb=" N   LEU A 355 "
           pdb=" CA  LEU A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.65  -48.35     0      5.00e+00 4.00e-02 9.35e+01
  dihedral pdb=" CA  ARG B 354 "
           pdb=" C   ARG B 354 "
           pdb=" N   LEU B 355 "
           pdb=" CA  LEU B 355 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -131.70  -48.30     0      5.00e+00 4.00e-02 9.33e+01
  dihedral pdb=" CA  CYS A 356 "
           pdb=" C   CYS A 356 "
           pdb=" N   PRO A 357 "
           pdb=" CA  PRO A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.63  -37.37     0      5.00e+00 4.00e-02 5.59e+01
  ... (remaining 5497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.016: 1424
       1.016 -    2.032: 0
       2.032 -    3.048: 0
       3.048 -    4.064: 0
       4.064 -    5.080: 2
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" C7  P1O B1003 "
            pdb=" C6  P1O B1003 "
            pdb=" C8  P1O B1003 "
            pdb=" O7  P1O B1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.35    2.73   -5.08 2.00e-01 2.50e+01 6.45e+02
  chirality pdb=" C7  P1O A1003 "
            pdb=" C6  P1O A1003 "
            pdb=" C8  P1O A1003 "
            pdb=" O7  P1O A1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.35    2.73   -5.08 2.00e-01 2.50e+01 6.45e+02
  chirality pdb=" CB  VAL A 531 "
            pdb=" CA  VAL A 531 "
            pdb=" CG1 VAL A 531 "
            pdb=" CG2 VAL A 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.11e+00
  ... (remaining 1423 not shown)

  Planarity restraints: 1564
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 670 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.52e+00
        pdb=" C   GLU A 670 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLU A 670 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   MET A 671 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 670 "    0.014 2.00e-02 2.50e+03   2.89e-02 8.36e+00
        pdb=" C   GLU B 670 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLU B 670 "    0.019 2.00e-02 2.50e+03
        pdb=" N   MET B 671 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 668 "    0.014 2.00e-02 2.50e+03   2.87e-02 8.24e+00
        pdb=" C   TYR A 668 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   TYR A 668 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A 669 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1561 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 516
        2.72 -     3.27: 9447
        3.27 -     3.81: 15769
        3.81 -     4.36: 18137
        4.36 -     4.90: 31147
  Nonbonded interactions: 75016
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 561 "
            pdb=" OG  SER A 565 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   VAL B 561 "
            pdb=" OG  SER B 565 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   ALA B 508 "
            pdb=" OG1 THR B 512 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   ALA A 508 "
            pdb=" OG1 THR A 512 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR A 364 "
            pdb=" OG  SER A 367 "
     model   vdw
     2.304 3.040
  ... (remaining 75011 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.340
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.770
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.122   9384  Z= 0.393
  Angle     :  1.016  11.295  12754  Z= 0.551
  Chirality :  0.198   5.080   1426
  Planarity :  0.009   0.069   1564
  Dihedral  : 15.204 139.337   3270
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.06 %
    Favored  : 93.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -3.36 (0.19), residues: 1110
  helix: -2.06 (0.14), residues: 760
  sheet:  None (None), residues: 0
  loop : -2.19 (0.26), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 252 
 TYR   0.042   0.003   TYR B 580 
 PHE   0.032   0.003   PHE B 685 
 TRP   0.017   0.003   TRP A 397 
 HIS   0.004   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00867 ( 9372)
  covalent geometry    : angle       1.01130 (12734)
  SS BOND              : bond        0.00618 (   10)
  SS BOND              : angle       2.70478 (   20)
  hydrogen bonds       : bond        0.12833 (  592)
  hydrogen bonds       : angle       7.51760 ( 1758)
  Misc. bond           : bond        0.00175 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 216
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLU cc_start: 0.8079 (tt0) cc_final: 0.7755 (tt0)
REVERT: A  355 LEU cc_start: 0.5820 (tp) cc_final: 0.5102 (pt)
REVERT: A  524 LEU cc_start: 0.8983 (tp) cc_final: 0.8671 (mt)
REVERT: A  534 MET cc_start: 0.7100 (mtm) cc_final: 0.6763 (mtt)
REVERT: A  650 TRP cc_start: 0.7373 (p90) cc_final: 0.6969 (p90)
REVERT: A  695 ASN cc_start: 0.8816 (t0) cc_final: 0.8504 (t0)
REVERT: A  730 GLN cc_start: 0.8584 (mt0) cc_final: 0.8269 (mm-40)
REVERT: A  818 HIS cc_start: 0.6650 (t-90) cc_final: 0.6259 (t70)
REVERT: B  294 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6223 (mm-30)
REVERT: B  355 LEU cc_start: 0.5826 (tp) cc_final: 0.5268 (pt)
REVERT: B  534 MET cc_start: 0.6973 (mtm) cc_final: 0.6653 (ptt)
REVERT: B  650 TRP cc_start: 0.7392 (p90) cc_final: 0.6960 (p90)
REVERT: B  661 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8274 (mmmm)
REVERT: B  730 GLN cc_start: 0.8561 (mt0) cc_final: 0.8262 (mm-40)
  outliers start: 2
  outliers final: 2
  residues processed: 216
  average time/residue: 0.0858
  time to fit residues: 26.1394
Evaluate side-chains
  150 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0270
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.6040

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

Flipped N/Q/H residues before XYZ refinement:
A 544 GLN
A 608 GLN
A 695 ASN
A 730 GLN
B 544 GLN
B 608 GLN
B 695 ASN
B 730 GLN
B 818 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.140824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.119813 restraints weight = 18673.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.122027 restraints weight = 11882.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.123340 restraints weight = 8877.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.124297 restraints weight = 7451.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.125043 restraints weight = 6601.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9384  Z= 0.151
  Angle     :  0.642   8.598  12754  Z= 0.342
  Chirality :  0.040   0.156   1426
  Planarity :  0.006   0.058   1564
  Dihedral  : 10.260 151.137   1308
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.90 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -1.17 (0.21), residues: 1110
  helix: -0.26 (0.16), residues: 750
  sheet:  None (None), residues: 0
  loop : -1.70 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 753 
 TYR   0.030   0.002   TYR B 477 
 PHE   0.026   0.002   PHE B 485 
 TRP   0.012   0.001   TRP A 397 
 HIS   0.008   0.001   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9372)
  covalent geometry    : angle       0.64030 (12734)
  SS BOND              : bond        0.00231 (   10)
  SS BOND              : angle       1.37316 (   20)
  hydrogen bonds       : bond        0.05291 (  592)
  hydrogen bonds       : angle       5.39090 ( 1758)
  Misc. bond           : bond        0.00062 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 SER cc_start: 0.8991 (p) cc_final: 0.8758 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 185
  average time/residue: 0.0828
  time to fit residues: 22.3663
Evaluate side-chains
  157 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  308 GLN
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  694 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0060
   chunk 14 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 5 optimal weight:   20.0000
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 818 HIS
B 695 ASN
B 818 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.140319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.119350 restraints weight = 18768.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.121592 restraints weight = 11859.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.123039 restraints weight = 8869.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.123845 restraints weight = 7335.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.124605 restraints weight = 6543.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9384  Z= 0.155
  Angle     :  0.597   8.631  12754  Z= 0.319
  Chirality :  0.040   0.145   1426
  Planarity :  0.005   0.054   1564
  Dihedral  :  9.689 150.552   1306
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.99 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -0.21 (0.23), residues: 1110
  helix:  0.44 (0.17), residues: 772
  sheet:  None (None), residues: 0
  loop : -1.33 (0.29), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 753 
 TYR   0.026   0.001   TYR B 477 
 PHE   0.023   0.002   PHE B 485 
 TRP   0.027   0.002   TRP B 650 
 HIS   0.008   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9372)
  covalent geometry    : angle       0.59642 (12734)
  SS BOND              : bond        0.00249 (   10)
  SS BOND              : angle       1.03215 (   20)
  hydrogen bonds       : bond        0.04938 (  592)
  hydrogen bonds       : angle       4.96972 ( 1758)
  Misc. bond           : bond        0.00038 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.8287 (t80) cc_final: 0.7591 (t80)
REVERT: A  322 LEU cc_start: 0.8390 (mm) cc_final: 0.7998 (tt)
REVERT: A  355 LEU cc_start: 0.5820 (tp) cc_final: 0.5324 (pt)
REVERT: B  305 TYR cc_start: 0.8331 (t80) cc_final: 0.7656 (t80)
REVERT: B  355 LEU cc_start: 0.5983 (tp) cc_final: 0.5539 (pt)
REVERT: B  474 ILE cc_start: 0.8239 (mm) cc_final: 0.7769 (mm)
REVERT: B  530 LYS cc_start: 0.7612 (mmtp) cc_final: 0.6367 (ttpt)
REVERT: B  534 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6372 (ptp)
  outliers start: 16
  outliers final: 14
  residues processed: 175
  average time/residue: 0.0768
  time to fit residues: 20.1104
Evaluate side-chains
  162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  308 GLN
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  694 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0040
   chunk 66 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.3998

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

Flipped N/Q/H residues before XYZ refinement:
A 695 ASN
B 695 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.139803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.118774 restraints weight = 19080.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.121065 restraints weight = 12045.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.122351 restraints weight = 8905.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.123325 restraints weight = 7436.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.124033 restraints weight = 6559.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9384  Z= 0.164
  Angle     :  0.599   8.689  12754  Z= 0.320
  Chirality :  0.040   0.148   1426
  Planarity :  0.005   0.053   1564
  Dihedral  :  9.549 150.937   1306
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.97 %
    Favored  : 81.83 %
  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 are not related in a simple way.
  whole:  0.25 (0.23), residues: 1110
  helix:  0.78 (0.18), residues: 772
  sheet:  None (None), residues: 0
  loop : -1.17 (0.29), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 753 
 TYR   0.029   0.002   TYR B 477 
 PHE   0.021   0.002   PHE B 485 
 TRP   0.010   0.001   TRP A 650 
 HIS   0.012   0.002   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9372)
  covalent geometry    : angle       0.59840 (12734)
  SS BOND              : bond        0.00257 (   10)
  SS BOND              : angle       0.93637 (   20)
  hydrogen bonds       : bond        0.04838 (  592)
  hydrogen bonds       : angle       4.82191 ( 1758)
  Misc. bond           : bond        0.00038 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  821 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6368 (pp20)
REVERT: A  826 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8127 (mp)
REVERT: B  322 LEU cc_start: 0.8296 (mm) cc_final: 0.7839 (tt)
REVERT: B  821 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6465 (pm20)
  outliers start: 20
  outliers final: 14
  residues processed: 179
  average time/residue: 0.0843
  time to fit residues: 22.1438
Evaluate side-chains
  161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  308 GLN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  821 GLU
Chi-restraints excluded: chain B residue  826 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 99 optimal weight:    0.1980
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 695 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.141965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.120514 restraints weight = 18820.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.122542 restraints weight = 11873.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.124112 restraints weight = 9014.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.125164 restraints weight = 7511.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.125655 restraints weight = 6561.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9384  Z= 0.134
  Angle     :  0.574   8.676  12754  Z= 0.305
  Chirality :  0.040   0.143   1426
  Planarity :  0.005   0.052   1564
  Dihedral  :  9.388 152.188   1306
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.08 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.24), residues: 1110
  helix:  1.09 (0.18), residues: 760
  sheet:  None (None), residues: 0
  loop : -1.16 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 753 
 TYR   0.026   0.001   TYR B 477 
 PHE   0.020   0.002   PHE B 485 
 TRP   0.009   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9372)
  covalent geometry    : angle       0.57312 (12734)
  SS BOND              : bond        0.00255 (   10)
  SS BOND              : angle       0.97839 (   20)
  hydrogen bonds       : bond        0.04583 (  592)
  hydrogen bonds       : angle       4.68050 ( 1758)
  Misc. bond           : bond        0.00037 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.8301 (t80) cc_final: 0.7739 (t80)
REVERT: A  322 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7999 (tt)
REVERT: A  373 ILE cc_start: 0.8364 (mt) cc_final: 0.8147 (mt)
REVERT: A  821 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6448 (pp20)
REVERT: A  826 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8009 (mp)
REVERT: B  305 TYR cc_start: 0.8289 (t80) cc_final: 0.7645 (t80)
REVERT: B  373 ILE cc_start: 0.8344 (mt) cc_final: 0.8053 (mt)
REVERT: B  812 PHE cc_start: 0.8096 (m-80) cc_final: 0.7865 (m-80)
REVERT: B  821 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6339 (pm20)
  outliers start: 29
  outliers final: 18
  residues processed: 191
  average time/residue: 0.0836
  time to fit residues: 23.5385
Evaluate side-chains
  172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  308 GLN
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  821 GLU
Chi-restraints excluded: chain B residue  826 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 74 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0370
   chunk 57 optimal weight:   30.0000
   chunk 100 optimal weight:    4.9990
   chunk 62 optimal weight:   20.0000
   chunk 61 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 97 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A 695 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.143467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.122547 restraints weight = 18668.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.124760 restraints weight = 11889.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.126055 restraints weight = 8908.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.127145 restraints weight = 7491.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.127826 restraints weight = 6573.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9384  Z= 0.125
  Angle     :  0.589  12.256  12754  Z= 0.304
  Chirality :  0.039   0.139   1426
  Planarity :  0.005   0.052   1564
  Dihedral  :  9.235 152.531   1306
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.84 %
    Favored  : 79.30 %
  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 are not related in a simple way.
  whole:  0.80 (0.24), residues: 1110
  helix:  1.24 (0.18), residues: 760
  sheet:  None (None), residues: 0
  loop : -0.97 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 753 
 TYR   0.027   0.001   TYR B 477 
 PHE   0.018   0.001   PHE B 485 
 TRP   0.012   0.001   TRP A 650 
 HIS   0.006   0.001   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9372)
  covalent geometry    : angle       0.58902 (12734)
  SS BOND              : bond        0.00158 (   10)
  SS BOND              : angle       0.81729 (   20)
  hydrogen bonds       : bond        0.04435 (  592)
  hydrogen bonds       : angle       4.58353 ( 1758)
  Misc. bond           : bond        0.00019 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8038 (tt)
REVERT: A  373 ILE cc_start: 0.8363 (mt) cc_final: 0.8066 (mt)
REVERT: A  553 MET cc_start: 0.7996 (tpp) cc_final: 0.7704 (tpp)
REVERT: A  812 PHE cc_start: 0.8109 (m-80) cc_final: 0.7831 (m-80)
REVERT: A  821 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6314 (pm20)
REVERT: B  322 LEU cc_start: 0.8406 (mm) cc_final: 0.7950 (tt)
REVERT: B  373 ILE cc_start: 0.8288 (mt) cc_final: 0.7984 (mt)
REVERT: B  812 PHE cc_start: 0.8096 (m-80) cc_final: 0.7828 (m-80)
REVERT: B  821 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6359 (pm20)
  outliers start: 26
  outliers final: 13
  residues processed: 185
  average time/residue: 0.0786
  time to fit residues: 21.6489
Evaluate side-chains
  171 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 155
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  821 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 95 optimal weight:    9.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.141564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.120131 restraints weight = 18964.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.122403 restraints weight = 12013.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.123714 restraints weight = 8943.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.124346 restraints weight = 7497.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.125237 restraints weight = 6826.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9384  Z= 0.165
  Angle     :  0.613  11.408  12754  Z= 0.319
  Chirality :  0.041   0.143   1426
  Planarity :  0.005   0.054   1564
  Dihedral  :  9.190 151.194   1306
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.28 %
    Favored  : 78.52 %
  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 are not related in a simple way.
  whole:  0.84 (0.24), residues: 1110
  helix:  1.19 (0.18), residues: 772
  sheet:  None (None), residues: 0
  loop : -0.81 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 753 
 TYR   0.025   0.001   TYR B 477 
 PHE   0.020   0.002   PHE B 838 
 TRP   0.019   0.001   TRP A 650 
 HIS   0.003   0.001   HIS A 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9372)
  covalent geometry    : angle       0.61220 (12734)
  SS BOND              : bond        0.00233 (   10)
  SS BOND              : angle       1.00303 (   20)
  hydrogen bonds       : bond        0.04590 (  592)
  hydrogen bonds       : angle       4.62734 ( 1758)
  Misc. bond           : bond        0.00033 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8013 (tt)
REVERT: A  373 ILE cc_start: 0.8326 (mt) cc_final: 0.8010 (mt)
REVERT: A  477 TYR cc_start: 0.6720 (OUTLIER) cc_final: 0.6243 (p90)
REVERT: A  553 MET cc_start: 0.8152 (tpp) cc_final: 0.7862 (tpp)
REVERT: A  753 ARG cc_start: 0.6933 (ptt90) cc_final: 0.6692 (ptt180)
REVERT: A  821 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6413 (pm20)
REVERT: A  842 MET cc_start: 0.8487 (ttt) cc_final: 0.8264 (ttt)
REVERT: B  322 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7972 (tt)
REVERT: B  373 ILE cc_start: 0.8337 (mt) cc_final: 0.8023 (mt)
REVERT: B  553 MET cc_start: 0.8139 (tpp) cc_final: 0.7795 (tpp)
REVERT: B  821 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6380 (pm20)
  outliers start: 29
  outliers final: 19
  residues processed: 178
  average time/residue: 0.0866
  time to fit residues: 22.6613
Evaluate side-chains
  169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  606 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  821 GLU
Chi-restraints excluded: chain B residue  826 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 695 ASN
B 695 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.142917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.121912 restraints weight = 18658.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.124105 restraints weight = 11997.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.125425 restraints weight = 9026.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.126476 restraints weight = 7573.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.127133 restraints weight = 6651.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9384  Z= 0.145
  Angle     :  0.605  12.290  12754  Z= 0.313
  Chirality :  0.041   0.158   1426
  Planarity :  0.005   0.054   1564
  Dihedral  :  9.176 152.006   1306
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.28 %
    Favored  : 78.52 %
  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 are not related in a simple way.
  whole:  0.95 (0.24), residues: 1110
  helix:  1.27 (0.18), residues: 772
  sheet:  None (None), residues: 0
  loop : -0.77 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 289 
 TYR   0.024   0.001   TYR B 477 
 PHE   0.020   0.001   PHE B 838 
 TRP   0.023   0.001   TRP A 650 
 HIS   0.005   0.001   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9372)
  covalent geometry    : angle       0.60451 (12734)
  SS BOND              : bond        0.00187 (   10)
  SS BOND              : angle       0.95468 (   20)
  hydrogen bonds       : bond        0.04559 (  592)
  hydrogen bonds       : angle       4.61169 ( 1758)
  Misc. bond           : bond        0.00026 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7932 (tt)
REVERT: A  373 ILE cc_start: 0.8321 (mt) cc_final: 0.8008 (mt)
REVERT: A  477 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.6166 (p90)
REVERT: A  821 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6362 (pm20)
REVERT: B  322 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7941 (tt)
REVERT: B  373 ILE cc_start: 0.8312 (mt) cc_final: 0.7986 (mt)
REVERT: B  821 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6372 (pm20)
  outliers start: 29
  outliers final: 19
  residues processed: 181
  average time/residue: 0.0737
  time to fit residues: 20.4289
Evaluate side-chains
  169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  606 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  695 ASN
Chi-restraints excluded: chain B residue  821 GLU
Chi-restraints excluded: chain B residue  826 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 96 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 93 optimal weight:    0.8980
   chunk 112 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 696 ASN
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 695 ASN
** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.144380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.123319 restraints weight = 18761.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.125548 restraints weight = 12004.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.126821 restraints weight = 9017.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.127529 restraints weight = 7592.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.128560 restraints weight = 6823.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9384  Z= 0.134
  Angle     :  0.607  11.165  12754  Z= 0.313
  Chirality :  0.041   0.148   1426
  Planarity :  0.005   0.054   1564
  Dihedral  :  9.158 152.504   1306
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.82 %
    Favored  : 77.53 %
  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 are not related in a simple way.
  whole:  0.97 (0.24), residues: 1110
  helix:  1.27 (0.18), residues: 772
  sheet:  None (None), residues: 0
  loop : -0.72 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 813 
 TYR   0.022   0.001   TYR B 477 
 PHE   0.016   0.001   PHE B 838 
 TRP   0.022   0.001   TRP B 650 
 HIS   0.008   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9372)
  covalent geometry    : angle       0.60588 (12734)
  SS BOND              : bond        0.00157 (   10)
  SS BOND              : angle       0.95451 (   20)
  hydrogen bonds       : bond        0.04509 (  592)
  hydrogen bonds       : angle       4.58702 ( 1758)
  Misc. bond           : bond        0.00013 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7947 (tt)
REVERT: A  373 ILE cc_start: 0.8342 (mt) cc_final: 0.8008 (mt)
REVERT: A  477 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6275 (p90)
REVERT: A  553 MET cc_start: 0.8133 (tpp) cc_final: 0.7834 (tpp)
REVERT: A  821 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6351 (pm20)
REVERT: B  322 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7919 (tt)
REVERT: B  373 ILE cc_start: 0.8294 (mt) cc_final: 0.7948 (mt)
REVERT: B  553 MET cc_start: 0.8121 (tpp) cc_final: 0.7787 (tpp)
REVERT: B  821 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6392 (pm20)
  outliers start: 24
  outliers final: 14
  residues processed: 178
  average time/residue: 0.0763
  time to fit residues: 20.3189
Evaluate side-chains
  173 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  821 GLU
Chi-restraints excluded: chain B residue  826 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 7 optimal weight:    7.9990
   chunk 37 optimal weight:    0.2980
   chunk 39 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 695 ASN
** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.144078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.122713 restraints weight = 18731.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.125042 restraints weight = 11878.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.126097 restraints weight = 8839.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.127246 restraints weight = 7529.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.128189 restraints weight = 6640.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   9384  Z= 0.145
  Angle     :  0.619  11.531  12754  Z= 0.317
  Chirality :  0.041   0.154   1426
  Planarity :  0.005   0.055   1564
  Dihedral  :  9.102 152.018   1306
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.15 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.24), residues: 1110
  helix:  1.36 (0.18), residues: 770
  sheet:  None (None), residues: 0
  loop : -0.75 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 753 
 TYR   0.022   0.001   TYR B 477 
 PHE   0.016   0.001   PHE B 838 
 TRP   0.023   0.001   TRP B 650 
 HIS   0.006   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9372)
  covalent geometry    : angle       0.61846 (12734)
  SS BOND              : bond        0.00197 (   10)
  SS BOND              : angle       0.93245 (   20)
  hydrogen bonds       : bond        0.04511 (  592)
  hydrogen bonds       : angle       4.57509 ( 1758)
  Misc. bond           : bond        0.00015 (    2)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7996 (tt)
REVERT: A  373 ILE cc_start: 0.8320 (mt) cc_final: 0.7977 (mt)
REVERT: A  477 TYR cc_start: 0.6575 (OUTLIER) cc_final: 0.6317 (p90)
REVERT: A  553 MET cc_start: 0.8147 (tpp) cc_final: 0.7834 (tpp)
REVERT: A  821 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6305 (pm20)
REVERT: B  322 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7900 (tt)
REVERT: B  373 ILE cc_start: 0.8299 (mt) cc_final: 0.7940 (mt)
REVERT: B  553 MET cc_start: 0.8174 (tpp) cc_final: 0.7842 (tpp)
REVERT: B  753 ARG cc_start: 0.6890 (ptt90) cc_final: 0.6616 (ptt180)
REVERT: B  821 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6373 (pm20)
  outliers start: 20
  outliers final: 15
  residues processed: 165
  average time/residue: 0.0753
  time to fit residues: 18.8288
Evaluate side-chains
  170 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  695 ASN
Chi-restraints excluded: chain B residue  821 GLU
Chi-restraints excluded: chain B residue  826 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 110 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 2 optimal weight:   20.0000
   chunk 75 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:   30.0000
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 695 ASN
** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.144104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.123011 restraints weight = 18557.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.125219 restraints weight = 12011.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.126448 restraints weight = 9093.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.127521 restraints weight = 7687.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.127521 restraints weight = 6784.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9384  Z= 0.142
  Angle     :  0.615  11.051  12754  Z= 0.316
  Chirality :  0.041   0.149   1426
  Planarity :  0.005   0.056   1564
  Dihedral  :  9.080 152.182   1306
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.15 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.24), residues: 1110
  helix:  1.37 (0.18), residues: 772
  sheet:  None (None), residues: 0
  loop : -0.68 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 813 
 TYR   0.022   0.001   TYR B 477 
 PHE   0.035   0.002   PHE B 462 
 TRP   0.022   0.001   TRP B 650 
 HIS   0.006   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9372)
  covalent geometry    : angle       0.61490 (12734)
  SS BOND              : bond        0.00182 (   10)
  SS BOND              : angle       0.90723 (   20)
  hydrogen bonds       : bond        0.04497 (  592)
  hydrogen bonds       : angle       4.56418 ( 1758)
  Misc. bond           : bond        0.00016 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1555.54 seconds
wall clock time: 27 minutes 38.11 seconds (1658.11 seconds total)