Starting phenix.real_space_refine
on Wed Feb  4 11:16:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7myn_24081/02_2026/7myn_24081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7myn_24081/02_2026/7myn_24081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7myn_24081/02_2026/7myn_24081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7myn_24081/02_2026/7myn_24081.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7myn_24081/02_2026/7myn_24081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7myn_24081/02_2026/7myn_24081.map"
  }
  resolution = 2.79
  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
-------------------------------------------------------------------------------
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=   0.394
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      73      5.16       5
     C    6633      2.51       5
     N    1800      2.21       5
     O    1920      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10426
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8072
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 977, 7981
          Classifications: {'peptide': 977}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 929}
          Chain breaks: 5
      Conformer: "B"
        Number of residues, atoms: 977, 7981
          Classifications: {'peptide': 977}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 929}
          Chain breaks: 5
          bond proxies already assigned to first conformer: 8063
    Chain: "B"
      Number of atoms: 2346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2346
          Classifications: {'peptide': 276}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 271}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
  Residues with excluded nonbonded symmetry interactions: 11
    residue:
      pdb=" N  AILE A 932 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD1BILE A 932 " occ=0.50
    residue:
      pdb=" N  AASP A 933 " occ=0.50
      ... (14 atoms not shown)
      pdb=" OD2BASP A 933 " occ=0.50
    residue:
      pdb=" N  APHE A 934 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 934 " occ=0.50
    residue:
      pdb=" N  AGLY A 935 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A 935 " occ=0.50
    residue:
      pdb=" N  AGLU A 950 " occ=0.54
      ... (16 atoms not shown)
      pdb=" OE2BGLU A 950 " occ=0.46
    residue:
      pdb=" N  AARG A 951 " occ=0.54
      ... (20 atoms not shown)
      pdb=" NH2BARG A 951 " occ=0.46
    residue:
      pdb=" N  AVAL A 952 " occ=0.54
      ... (12 atoms not shown)
      pdb=" CG2BVAL A 952 " occ=0.46
    residue:
      pdb=" N  APRO A 953 " occ=0.54
      ... (12 atoms not shown)
      pdb=" CD BPRO A 953 " occ=0.46
    residue:
      pdb=" N  APHE A 954 " occ=0.54
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 954 " occ=0.46
    residue:
      pdb=" N  AVAL A 955 " occ=0.54
      ... (12 atoms not shown)
      pdb=" CG2BVAL A 955 " occ=0.46
    residue:
      pdb=" N  ALEU A 956 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD2BLEU A 956 " occ=0.50
  Time building chain proxies: 3.73, per 1000 atoms: 0.36
  Number of scatterers: 10426
  At special positions: 0
  Unit cell: (86.735, 129.58, 110.77, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      73     16.00
     O    1920      8.00
     N    1800      7.00
     C    6633      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 754.8 milliseconds
  

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2418

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      52.5% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 52
      removed outlier: 3.765A  pdb=" N   GLU A  52 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
    Processing helix  chain 'A' and resid 89 through 93
      removed outlier: 4.021A  pdb=" N   ARG A  93 " --> pdb=" O   CYS A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 122
    Processing helix  chain 'A' and resid 125 through 131
    Processing helix  chain 'A' and resid 133 through 155
      removed outlier: 4.113A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 297
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.634A  pdb=" N   SER A 308 " --> pdb=" O   PRO A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 496
    Processing helix  chain 'A' and resid 528 through 537
      removed outlier: 3.666A  pdb=" N   LYS A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 556 through 563
      removed outlier: 3.886A  pdb=" N   VAL A 559 " --> pdb=" O   HIS A 556 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR A 560 " --> pdb=" O   TYR A 557 " (cutoff:3.500A)
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 572
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 3.634A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 600 through 603
    Processing helix  chain 'A' and resid 608 through 622
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 647 through 658
      removed outlier: 3.575A  pdb=" N   ARG A 651 " --> pdb=" O   ASN A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 673
      removed outlier: 3.773A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 721
      removed outlier: 3.884A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 741
      removed outlier: 3.844A  pdb=" N   ARG A 741 " --> pdb=" O   GLU A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 749
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 857 through 865
    Processing helix  chain 'A' and resid 875 through 885
      removed outlier: 3.573A  pdb=" N   ASN A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 888
      No H-bonds generated for 'chain 'A' and resid 886 through 888'
    Processing helix  chain 'A' and resid 889 through 912
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 4.018A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 994
    Processing helix  chain 'A' and resid 994 through 1004
      removed outlier: 3.729A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1009
      removed outlier: 3.554A  pdb=" N   SER A1008 " --> pdb=" O   MET A1005 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1005 through 1009'
    Processing helix  chain 'A' and resid 1015 through 1026
      removed outlier: 3.932A  pdb=" N   ILE A1019 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   TYR A1021 " --> pdb=" O   ASP A1017 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ILE A1022 " --> pdb=" O   ASP A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1048
      removed outlier: 4.087A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 331
    Processing helix  chain 'B' and resid 339 through 347
      removed outlier: 3.622A  pdb=" N   VAL B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 4.161A  pdb=" N   GLY B 388 " --> pdb=" O   HIS B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 412 through 416
      removed outlier: 3.922A  pdb=" N   GLN B 415 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 436
      removed outlier: 3.745A  pdb=" N   GLN B 435 " --> pdb=" O   GLN B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 507
      removed outlier: 4.691A  pdb=" N   GLU B 507 " --> pdb=" O   ARG B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.656A  pdb=" N   PHE B 512 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 587
      removed outlier: 3.880A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
    Processing helix  chain 'B' and resid 590 through 596
      removed outlier: 3.695A  pdb=" N   LEU B 594 " --> pdb=" O   ARG B 590 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU B 596 " --> pdb=" O   LYS B 592 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
      removed outlier: 3.844A  pdb=" N   ILE A  20 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82
      removed outlier: 4.154A  pdb=" N   PHE A  70 " --> pdb=" O   PHE A  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 211
    Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261
      removed outlier: 4.201A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.382A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.870A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 372
      removed outlier: 5.085A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   SER A 408 " --> pdb=" O   PRO A 421 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   LYS A 410 " --> pdb=" O   HIS A 419 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   HIS A 419 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 779 through 783
      removed outlier: 6.706A  pdb=" N   VAL A 845 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AB1, first strand: chain 'B' and resid 334 through 336

    515 hydrogen bonds defined for protein.
    1467 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: 1.65

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3427
        1.35 -     1.46: 2328
        1.46 -     1.58: 4770
        1.58 -     1.70: 0
        1.70 -     1.82: 114
  Bond restraints: 10639
  Sorted by residual:
  bond pdb=" CB  ASN A 157 "
       pdb=" CG  ASN A 157 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 2.50e-02 1.60e+03 1.65e+00
  bond pdb=" CA  LYS A 264 "
       pdb=" CB  LYS A 264 "
    ideal  model  delta    sigma   weight residual
    1.526  1.541 -0.016 1.25e-02 6.40e+03 1.55e+00
  bond pdb=" CB  ASN A 803 "
       pdb=" CG  ASN A 803 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.51e+00
  bond pdb=" CD  GLU B 458 "
       pdb=" OE1 GLU B 458 "
    ideal  model  delta    sigma   weight residual
    1.249  1.226  0.023 1.90e-02 2.77e+03 1.43e+00
  bond pdb=" CA  ASN A 157 "
       pdb=" CB  ASN A 157 "
    ideal  model  delta    sigma   weight residual
    1.526  1.544 -0.019 1.68e-02 3.54e+03 1.24e+00
  ... (remaining 10634 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 14040
        2.17 -     4.33: 262
        4.33 -     6.50: 40
        6.50 -     8.67: 8
        8.67 -    10.84: 2
  Bond angle restraints: 14352
  Sorted by residual:
  angle pdb=" N   VAL A 105 "
        pdb=" CA  VAL A 105 "
        pdb=" C   VAL A 105 "
      ideal   model   delta    sigma   weight residual
     113.20  108.84    4.36 9.60e-01 1.09e+00 2.06e+01
  angle pdb=" C   ILE A 102 "
        pdb=" N   GLU A 103 "
        pdb=" CA  GLU A 103 "
      ideal   model   delta    sigma   weight residual
     121.03  128.10   -7.07 1.60e+00 3.91e-01 1.96e+01
  angle pdb=" N   GLU B 458 "
        pdb=" CA  GLU B 458 "
        pdb=" CB  GLU B 458 "
      ideal   model   delta    sigma   weight residual
     110.16  116.28   -6.12 1.48e+00 4.57e-01 1.71e+01
  angle pdb=" N   ASN A 157 "
        pdb=" CA  ASN A 157 "
        pdb=" C   ASN A 157 "
      ideal   model   delta    sigma   weight residual
     110.44  106.22    4.22 1.20e+00 6.94e-01 1.24e+01
  angle pdb=" CA  TYR A 265 "
        pdb=" CB  TYR A 265 "
        pdb=" CG  TYR A 265 "
      ideal   model   delta    sigma   weight residual
     113.90  119.87   -5.97 1.80e+00 3.09e-01 1.10e+01
  ... (remaining 14347 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5830
       17.97 -    35.93: 573
       35.93 -    53.90: 78
       53.90 -    71.86: 18
       71.86 -    89.83: 9
  Dihedral angle restraints: 6508
    sinusoidal: 2781
      harmonic: 3727
  Sorted by residual:
  dihedral pdb=" CA  GLU A  81 "
           pdb=" C   GLU A  81 "
           pdb=" N   PHE A  82 "
           pdb=" CA  PHE A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.29  -23.71     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  GLU A  48 "
           pdb=" C   GLU A  48 "
           pdb=" N   LEU A  49 "
           pdb=" CA  LEU A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.28   22.72     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  SER A 405 "
           pdb=" C   SER A 405 "
           pdb=" N   ILE A 406 "
           pdb=" CA  ILE A 406 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.91   18.09     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 6505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1084
       0.041 -    0.082: 347
       0.082 -    0.124: 93
       0.124 -    0.165: 24
       0.165 -    0.206: 3
  Chirality restraints: 1551
  Sorted by residual:
  chirality pdb=" CA  GLU A 223 "
            pdb=" N   GLU A 223 "
            pdb=" C   GLU A 223 "
            pdb=" CB  GLU A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  GLU A  48 "
            pdb=" N   GLU A  48 "
            pdb=" C   GLU A  48 "
            pdb=" CB  GLU A  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.71e-01
  chirality pdb=" CA  ILE A 338 "
            pdb=" N   ILE A 338 "
            pdb=" C   ILE A 338 "
            pdb=" CB  ILE A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.07e-01
  ... (remaining 1548 not shown)

  Planarity restraints: 1848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 708 "    0.013 2.00e-02 2.50e+03   2.57e-02 6.62e+00
        pdb=" C   ALA A 708 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ALA A 708 "    0.017 2.00e-02 2.50e+03
        pdb=" N   MET A 709 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 195 "    0.017 2.00e-02 2.50e+03   1.60e-02 6.42e+00
        pdb=" CG  TRP A 195 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 195 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 195 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 195 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 195 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 195 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 195 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 195 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 195 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 707 "    0.012 2.00e-02 2.50e+03   2.38e-02 5.66e+00
        pdb=" C   GLU A 707 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLU A 707 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 708 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1845 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2664
        2.80 -     3.33: 10112
        3.33 -     3.85: 17934
        3.85 -     4.38: 20765
        4.38 -     4.90: 35084
  Nonbonded interactions: 86559
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 430 "
            pdb=" OH  TYR A 644 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A 584 "
            pdb=" OD1 ASP A 608 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR A  41 "
            pdb=" O   GLU A  85 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O  BARG A 951 "
            pdb=" OH  TYR A1021 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OD1 ASP A 454 "
            pdb=" NH1 ARG B 348 "
     model   vdw
     2.303 3.120
  ... (remaining 86554 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.46 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     12.510
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:7.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10639  Z= 0.148
  Angle     :  0.712  10.836  14352  Z= 0.372
  Chirality :  0.045   0.206   1551
  Planarity :  0.005   0.044   1848
  Dihedral  : 14.110  89.827   4090
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.43 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.41 (0.22), residues: 1252
  helix:  0.43 (0.20), residues: 577
  sheet: -1.13 (0.42), residues: 138
  loop : -0.68 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 382 
 TYR   0.024   0.001   TYR A 207 
 PHE   0.017   0.002   PHE A 734 
 TRP   0.043   0.002   TRP A 195 
 HIS   0.003   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10639)
  covalent geometry    : angle       0.71186 (14352)
  hydrogen bonds       : bond        0.12279 (  510)
  hydrogen bonds       : angle       5.38272 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 331
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 HIS cc_start: 0.8156 (p90) cc_final: 0.7913 (p90)
REVERT: A   78 GLU cc_start: 0.7172 (pp20) cc_final: 0.6967 (pp20)
REVERT: A   81 GLU cc_start: 0.7894 (pp20) cc_final: 0.7308 (pp20)
REVERT: A   83 PHE cc_start: 0.7518 (m-80) cc_final: 0.6542 (m-80)
REVERT: A   85 GLU cc_start: 0.7884 (mp0) cc_final: 0.7414 (mp0)
REVERT: A  179 LYS cc_start: 0.8412 (mppt) cc_final: 0.8139 (mppt)
REVERT: A  191 ILE cc_start: 0.8659 (mm) cc_final: 0.8293 (mp)
REVERT: A  195 TRP cc_start: 0.8108 (m100) cc_final: 0.7615 (m100)
REVERT: A  205 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7369 (pp30)
REVERT: A  219 GLN cc_start: 0.8296 (pt0) cc_final: 0.8075 (pt0)
REVERT: A  264 LYS cc_start: 0.8014 (ptmm) cc_final: 0.7721 (pptt)
REVERT: A  710 GLU cc_start: 0.7644 (pp20) cc_final: 0.7314 (pp20)
REVERT: A  882 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7998 (mmmt)
REVERT: A  976 GLU cc_start: 0.7297 (mp0) cc_final: 0.6930 (mm-30)
REVERT: A 1010 MET cc_start: 0.7458 (mpp) cc_final: 0.6927 (mpt)
REVERT: B  326 MET cc_start: 0.6988 (tpp) cc_final: 0.6073 (tpp)
REVERT: B  485 GLU cc_start: 0.8044 (tp30) cc_final: 0.7688 (tp30)
REVERT: B  496 GLU cc_start: 0.8508 (tp30) cc_final: 0.7864 (tp30)
REVERT: B  499 GLN cc_start: 0.7424 (tm-30) cc_final: 0.6974 (tm-30)
REVERT: B  525 MET cc_start: 0.7838 (mmp) cc_final: 0.7349 (mmp)
REVERT: B  535 ILE cc_start: 0.8755 (pt) cc_final: 0.8464 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 331
  average time/residue: 0.5576
  time to fit residues: 198.4883
Evaluate side-chains
  246 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0020
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:    0.7980
   chunk 123 optimal weight:   50.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.1392

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 157 ASN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
A 630 GLN
A 728 GLN
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 958 GLN
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.170970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.113374 restraints weight = 14431.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 3.05
r_work: 0.3167 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10639  Z= 0.153
  Angle     :  0.642  10.134  14352  Z= 0.323
  Chirality :  0.042   0.148   1551
  Planarity :  0.004   0.039   1848
  Dihedral  :  4.584  44.794   1388
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.04 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.22 (0.23), residues: 1252
  helix:  1.08 (0.21), residues: 594
  sheet: -1.04 (0.40), residues: 161
  loop : -0.47 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 108 
 TYR   0.017   0.001   TYR B 426 
 PHE   0.027   0.002   PHE A  83 
 TRP   0.028   0.002   TRP A 195 
 HIS   0.003   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10639)
  covalent geometry    : angle       0.64207 (14352)
  hydrogen bonds       : bond        0.03663 (  510)
  hydrogen bonds       : angle       4.13439 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 260
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 HIS cc_start: 0.8339 (p90) cc_final: 0.8121 (p90)
REVERT: A   81 GLU cc_start: 0.8008 (pp20) cc_final: 0.7102 (pp20)
REVERT: A   83 PHE cc_start: 0.8043 (m-80) cc_final: 0.7332 (m-80)
REVERT: A  111 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8360 (mtpt)
REVERT: A  130 MET cc_start: 0.7997 (tmm) cc_final: 0.7730 (pp-130)
REVERT: A  157 ASN cc_start: 0.6959 (t0) cc_final: 0.6551 (t0)
REVERT: A  162 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7983 (mtp85)
REVERT: A  205 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7127 (pp30)
REVERT: A  264 LYS cc_start: 0.8325 (ptmm) cc_final: 0.7885 (ptmm)
REVERT: A  286 MET cc_start: 0.7141 (mmm) cc_final: 0.6936 (mmp)
REVERT: A  365 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8122 (pp20)
REVERT: A  490 SER cc_start: 0.8741 (m) cc_final: 0.8483 (m)
REVERT: A  677 ASN cc_start: 0.8675 (t0) cc_final: 0.8091 (t0)
REVERT: A  740 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8318 (tpp80)
REVERT: A  741 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7834 (ttp-110)
REVERT: A  852 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.7975 (ptp90)
REVERT: A 1037 GLU cc_start: 0.8102 (mp0) cc_final: 0.7826 (mp0)
REVERT: B  386 ARG cc_start: 0.6940 (ttp-110) cc_final: 0.6623 (ttp-110)
REVERT: B  452 TYR cc_start: 0.7628 (m-80) cc_final: 0.7302 (m-80)
REVERT: B  496 GLU cc_start: 0.8660 (tp30) cc_final: 0.7919 (tp30)
REVERT: B  499 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6946 (tm-30)
REVERT: B  535 ILE cc_start: 0.8623 (pt) cc_final: 0.8344 (pp)
REVERT: B  540 ASP cc_start: 0.7896 (t0) cc_final: 0.7321 (t70)
REVERT: B  560 ASP cc_start: 0.8009 (t0) cc_final: 0.7785 (t70)
  outliers start: 26
  outliers final: 7
  residues processed: 271
  average time/residue: 0.5917
  time to fit residues: 172.4163
Evaluate side-chains
  249 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 240
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  550 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 120 optimal weight:   20.0000
   chunk 99 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 86 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 98 optimal weight:    8.9990
   chunk 104 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 450 HIS
A 728 GLN
A 958 GLN
B 385 HIS
B 488 ASN
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.166498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110439 restraints weight = 14856.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.94
r_work: 0.3114 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  10639  Z= 0.258
  Angle     :  0.669   9.396  14352  Z= 0.337
  Chirality :  0.044   0.160   1551
  Planarity :  0.004   0.036   1848
  Dihedral  :  4.757  53.032   1388
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.88 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.29 (0.24), residues: 1252
  helix:  1.17 (0.21), residues: 598
  sheet: -1.17 (0.40), residues: 146
  loop : -0.45 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 741 
 TYR   0.017   0.002   TYR A 207 
 PHE   0.036   0.002   PHE B 456 
 TRP   0.024   0.002   TRP A 195 
 HIS   0.012   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 (10639)
  covalent geometry    : angle       0.66866 (14352)
  hydrogen bonds       : bond        0.03931 (  510)
  hydrogen bonds       : angle       4.10441 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 247
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 ASN cc_start: 0.7213 (t0) cc_final: 0.6848 (t0)
REVERT: A  205 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6900 (pp30)
REVERT: A  264 LYS cc_start: 0.8598 (ptmm) cc_final: 0.8190 (ptmm)
REVERT: A  286 MET cc_start: 0.7294 (mmm) cc_final: 0.7072 (mmp)
REVERT: A  365 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8127 (pp20)
REVERT: A  382 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7938 (tpt-90)
REVERT: A  474 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8004 (mp0)
REVERT: A  677 ASN cc_start: 0.8664 (t0) cc_final: 0.8053 (t0)
REVERT: A  728 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7290 (tm-30)
REVERT: A  732 MET cc_start: 0.8894 (mmm) cc_final: 0.8593 (mmm)
REVERT: A  740 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8278 (tpp80)
REVERT: A  741 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8045 (ttm110)
REVERT: A  805 ASP cc_start: 0.8047 (m-30) cc_final: 0.7783 (p0)
REVERT: A  809 GLN cc_start: 0.8787 (mp10) cc_final: 0.8493 (mp10)
REVERT: A 1010 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.6412 (mpt)
REVERT: B  386 ARG cc_start: 0.7012 (ttp-110) cc_final: 0.6721 (ttp-110)
REVERT: B  458 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8319 (pm20)
REVERT: B  496 GLU cc_start: 0.8757 (tp30) cc_final: 0.7997 (tp30)
REVERT: B  499 GLN cc_start: 0.7483 (tm-30) cc_final: 0.6994 (tm-30)
REVERT: B  525 MET cc_start: 0.8132 (mmp) cc_final: 0.7724 (mmp)
REVERT: B  535 ILE cc_start: 0.8678 (pt) cc_final: 0.8385 (pp)
REVERT: B  540 ASP cc_start: 0.7873 (t0) cc_final: 0.7370 (t70)
REVERT: B  560 ASP cc_start: 0.8073 (t0) cc_final: 0.7741 (t0)
  outliers start: 35
  outliers final: 8
  residues processed: 261
  average time/residue: 0.5616
  time to fit residues: 158.1774
Evaluate side-chains
  241 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 227
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  458 GLU
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   chunk 104 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 93 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 205 GLN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 450 HIS
A 630 GLN
A 647 ASN
A 728 GLN
** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 958 GLN
B 385 HIS
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.168382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.112911 restraints weight = 15928.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 3.05
r_work: 0.3146 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10639  Z= 0.152
  Angle     :  0.607   9.646  14352  Z= 0.304
  Chirality :  0.042   0.181   1551
  Planarity :  0.004   0.036   1848
  Dihedral  :  4.488  41.518   1388
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.47 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.48 (0.24), residues: 1252
  helix:  1.34 (0.21), residues: 600
  sheet: -1.12 (0.41), residues: 146
  loop : -0.38 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 852 
 TYR   0.014   0.001   TYR B 556 
 PHE   0.034   0.002   PHE B 456 
 TRP   0.026   0.001   TRP A 195 
 HIS   0.004   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10639)
  covalent geometry    : angle       0.60694 (14352)
  hydrogen bonds       : bond        0.03490 (  510)
  hydrogen bonds       : angle       3.99149 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 240
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLU cc_start: 0.7886 (pp20) cc_final: 0.6934 (pp20)
REVERT: A  157 ASN cc_start: 0.7156 (t0) cc_final: 0.6800 (t0)
REVERT: A  205 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7091 (pp30)
REVERT: A  264 LYS cc_start: 0.8488 (ptmm) cc_final: 0.8047 (ptmm)
REVERT: A  382 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7959 (tpt-90)
REVERT: A  432 TYR cc_start: 0.9084 (p90) cc_final: 0.8773 (p90)
REVERT: A  488 ASP cc_start: 0.7952 (t0) cc_final: 0.7705 (t70)
REVERT: A  494 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8052 (tm-30)
REVERT: A  677 ASN cc_start: 0.8606 (t0) cc_final: 0.8016 (t0)
REVERT: A  732 MET cc_start: 0.8886 (mmm) cc_final: 0.8681 (mmm)
REVERT: A  741 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8002 (ttp-110)
REVERT: A  805 ASP cc_start: 0.7982 (m-30) cc_final: 0.7768 (p0)
REVERT: A  825 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7784 (mp-120)
REVERT: A  852 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8164 (ptp90)
REVERT: A 1037 GLU cc_start: 0.8277 (mp0) cc_final: 0.7953 (mp0)
REVERT: B  386 ARG cc_start: 0.6872 (ttp-110) cc_final: 0.6598 (ttp-110)
REVERT: B  458 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8322 (pm20)
REVERT: B  466 LEU cc_start: 0.8599 (mm) cc_final: 0.8376 (mt)
REVERT: B  496 GLU cc_start: 0.8749 (tp30) cc_final: 0.7962 (tp30)
REVERT: B  499 GLN cc_start: 0.7484 (tm-30) cc_final: 0.6992 (tm-30)
REVERT: B  525 MET cc_start: 0.8085 (mmp) cc_final: 0.7637 (mmp)
REVERT: B  535 ILE cc_start: 0.8675 (pt) cc_final: 0.8373 (pp)
REVERT: B  540 ASP cc_start: 0.7845 (t0) cc_final: 0.7387 (t70)
REVERT: B  560 ASP cc_start: 0.8176 (t0) cc_final: 0.7737 (t0)
  outliers start: 34
  outliers final: 14
  residues processed: 253
  average time/residue: 0.5181
  time to fit residues: 141.5112
Evaluate side-chains
  243 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 226
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  390 ASP
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  458 GLU
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 0 optimal weight:   50.0000
   chunk 113 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 117 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 99 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  75 GLN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
A 630 GLN
A 728 GLN
** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 385 HIS
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.167700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.112434 restraints weight = 13900.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.86
r_work: 0.3143 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10639  Z= 0.179
  Angle     :  0.625  10.125  14352  Z= 0.313
  Chirality :  0.043   0.142   1551
  Planarity :  0.004   0.039   1848
  Dihedral  :  4.410  27.900   1388
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.07 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.52 (0.24), residues: 1252
  helix:  1.43 (0.21), residues: 597
  sheet: -1.16 (0.41), residues: 146
  loop : -0.41 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 852 
 TYR   0.018   0.001   TYR A 622 
 PHE   0.037   0.002   PHE B 456 
 TRP   0.025   0.002   TRP A 195 
 HIS   0.005   0.001   HIS B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (10639)
  covalent geometry    : angle       0.62544 (14352)
  hydrogen bonds       : bond        0.03533 (  510)
  hydrogen bonds       : angle       3.94820 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 243
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.8228 (pp20) cc_final: 0.7570 (pp20)
REVERT: A   83 PHE cc_start: 0.7940 (m-80) cc_final: 0.7656 (m-10)
REVERT: A   85 GLU cc_start: 0.7849 (pp20) cc_final: 0.7566 (pp20)
REVERT: A  157 ASN cc_start: 0.7219 (t0) cc_final: 0.6865 (t0)
REVERT: A  264 LYS cc_start: 0.8495 (ptmm) cc_final: 0.8132 (ptmm)
REVERT: A  286 MET cc_start: 0.7852 (mmp) cc_final: 0.7441 (mmp)
REVERT: A  336 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9068 (mp)
REVERT: A  382 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7868 (tpt-90)
REVERT: A  432 TYR cc_start: 0.9093 (p90) cc_final: 0.8705 (p90)
REVERT: A  474 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7838 (mp0)
REVERT: A  488 ASP cc_start: 0.7963 (t0) cc_final: 0.7722 (t70)
REVERT: A  494 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8053 (tm-30)
REVERT: A  546 GLN cc_start: 0.9131 (mp10) cc_final: 0.8812 (mp10)
REVERT: A  677 ASN cc_start: 0.8594 (t0) cc_final: 0.7999 (t0)
REVERT: A  852 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8171 (ptp90)
REVERT: A 1037 GLU cc_start: 0.8322 (mp0) cc_final: 0.7925 (mp0)
REVERT: B  330 ASP cc_start: 0.8346 (p0) cc_final: 0.7699 (p0)
REVERT: B  364 MET cc_start: 0.7031 (pmm) cc_final: 0.6397 (pmm)
REVERT: B  367 ASP cc_start: 0.6468 (m-30) cc_final: 0.5774 (m-30)
REVERT: B  386 ARG cc_start: 0.6845 (ttp-110) cc_final: 0.6502 (ttp-110)
REVERT: B  496 GLU cc_start: 0.8733 (tp30) cc_final: 0.7955 (tp30)
REVERT: B  499 GLN cc_start: 0.7502 (tm-30) cc_final: 0.6965 (tm-30)
REVERT: B  525 MET cc_start: 0.8154 (mmp) cc_final: 0.7736 (mmp)
REVERT: B  535 ILE cc_start: 0.8692 (pt) cc_final: 0.8376 (pp)
REVERT: B  540 ASP cc_start: 0.7945 (t0) cc_final: 0.7455 (t70)
REVERT: B  560 ASP cc_start: 0.8279 (t0) cc_final: 0.7770 (t0)
  outliers start: 34
  outliers final: 15
  residues processed: 259
  average time/residue: 0.6086
  time to fit residues: 169.5958
Evaluate side-chains
  247 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 230
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 40 optimal weight:    0.0770
   chunk 82 optimal weight:   10.0000
   chunk 91 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 99 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 110 optimal weight:    9.9990
   chunk 123 optimal weight:   10.0000
   overall best weight:    1.7342

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A  75 GLN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
A 630 GLN
A 738 GLN
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.169555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.113825 restraints weight = 17590.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.21
r_work: 0.3149 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10639  Z= 0.135
  Angle     :  0.610  10.736  14352  Z= 0.304
  Chirality :  0.042   0.231   1551
  Planarity :  0.004   0.041   1848
  Dihedral  :  4.271  28.212   1385
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.59 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.64 (0.24), residues: 1252
  helix:  1.59 (0.21), residues: 593
  sheet: -1.12 (0.42), residues: 146
  loop : -0.41 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 979 
 TYR   0.019   0.001   TYR A 622 
 PHE   0.038   0.002   PHE B 456 
 TRP   0.025   0.001   TRP A 479 
 HIS   0.006   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10639)
  covalent geometry    : angle       0.60984 (14352)
  hydrogen bonds       : bond        0.03350 (  510)
  hydrogen bonds       : angle       3.89424 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 248
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8402 (p90) cc_final: 0.7918 (p90)
REVERT: A   81 GLU cc_start: 0.8124 (pp20) cc_final: 0.7516 (pp20)
REVERT: A   83 PHE cc_start: 0.7855 (m-80) cc_final: 0.7564 (m-10)
REVERT: A   85 GLU cc_start: 0.7998 (pp20) cc_final: 0.7693 (pp20)
REVERT: A  149 GLU cc_start: 0.8092 (tt0) cc_final: 0.7867 (tm-30)
REVERT: A  157 ASN cc_start: 0.7162 (t0) cc_final: 0.6813 (t0)
REVERT: A  205 GLN cc_start: 0.7680 (pt0) cc_final: 0.7107 (pp30)
REVERT: A  206 LYS cc_start: 0.9002 (ptpp) cc_final: 0.8763 (ptpp)
REVERT: A  264 LYS cc_start: 0.8477 (ptmm) cc_final: 0.8124 (ptmm)
REVERT: A  286 MET cc_start: 0.7579 (mmp) cc_final: 0.6974 (mmp)
REVERT: A  304 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8315 (tpp)
REVERT: A  382 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7925 (tpt-90)
REVERT: A  432 TYR cc_start: 0.9064 (p90) cc_final: 0.8700 (p90)
REVERT: A  474 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7830 (mp0)
REVERT: A  488 ASP cc_start: 0.7984 (t0) cc_final: 0.7710 (t70)
REVERT: A  494 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8019 (tm-30)
REVERT: A  546 GLN cc_start: 0.9130 (mp10) cc_final: 0.8822 (mp10)
REVERT: A  677 ASN cc_start: 0.8583 (t0) cc_final: 0.8014 (t0)
REVERT: A  728 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6464 (tp40)
REVERT: A  740 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8267 (tpp80)
REVERT: A  741 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7899 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7844 (mm-40)
REVERT: A  852 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8150 (ptp90)
REVERT: A 1037 GLU cc_start: 0.8316 (mp0) cc_final: 0.7976 (mp0)
REVERT: B  386 ARG cc_start: 0.6848 (ttp-110) cc_final: 0.6517 (ttp-110)
REVERT: B  466 LEU cc_start: 0.8825 (mm) cc_final: 0.8593 (mt)
REVERT: B  496 GLU cc_start: 0.8739 (tp30) cc_final: 0.7960 (tp30)
REVERT: B  499 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7012 (tm-30)
REVERT: B  525 MET cc_start: 0.8109 (mmp) cc_final: 0.7702 (mmp)
REVERT: B  535 ILE cc_start: 0.8684 (pt) cc_final: 0.8369 (pp)
REVERT: B  540 ASP cc_start: 0.7959 (t0) cc_final: 0.7483 (t70)
REVERT: B  560 ASP cc_start: 0.8301 (t0) cc_final: 0.7997 (t0)
  outliers start: 31
  outliers final: 14
  residues processed: 261
  average time/residue: 0.5978
  time to fit residues: 168.4262
Evaluate side-chains
  247 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 228
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 76 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 213 HIS
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
A 630 GLN
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.169925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.114331 restraints weight = 15704.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 3.04
r_work: 0.3164 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10639  Z= 0.142
  Angle     :  0.619  11.010  14352  Z= 0.311
  Chirality :  0.042   0.193   1551
  Planarity :  0.004   0.042   1848
  Dihedral  :  4.310  29.061   1385
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.71 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.71 (0.24), residues: 1252
  helix:  1.66 (0.21), residues: 593
  sheet: -1.24 (0.41), residues: 152
  loop : -0.32 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 108 
 TYR   0.023   0.001   TYR A 622 
 PHE   0.036   0.002   PHE B 456 
 TRP   0.027   0.001   TRP A 479 
 HIS   0.011   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10639)
  covalent geometry    : angle       0.61946 (14352)
  hydrogen bonds       : bond        0.03410 (  510)
  hydrogen bonds       : angle       3.90227 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 237
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8382 (p90) cc_final: 0.7927 (p90)
REVERT: A   81 GLU cc_start: 0.8126 (pp20) cc_final: 0.7405 (pp20)
REVERT: A   83 PHE cc_start: 0.7898 (m-80) cc_final: 0.7464 (m-10)
REVERT: A   85 GLU cc_start: 0.8056 (pp20) cc_final: 0.7786 (pp20)
REVERT: A  149 GLU cc_start: 0.8045 (tt0) cc_final: 0.7807 (tm-30)
REVERT: A  157 ASN cc_start: 0.7173 (t0) cc_final: 0.6826 (t0)
REVERT: A  172 GLU cc_start: 0.7038 (pp20) cc_final: 0.6770 (pp20)
REVERT: A  195 TRP cc_start: 0.8047 (m100) cc_final: 0.7797 (m100)
REVERT: A  205 GLN cc_start: 0.7627 (pt0) cc_final: 0.7074 (pp30)
REVERT: A  264 LYS cc_start: 0.8492 (ptmm) cc_final: 0.8096 (ptmm)
REVERT: A  286 MET cc_start: 0.7540 (mmp) cc_final: 0.7021 (mmp)
REVERT: A  304 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8283 (tpp)
REVERT: A  382 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7922 (tpt-90)
REVERT: A  432 TYR cc_start: 0.9037 (p90) cc_final: 0.8664 (p90)
REVERT: A  474 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7818 (mp0)
REVERT: A  488 ASP cc_start: 0.7950 (t0) cc_final: 0.7648 (t70)
REVERT: A  494 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8022 (tm-30)
REVERT: A  546 GLN cc_start: 0.9117 (mp10) cc_final: 0.8803 (mp10)
REVERT: A  677 ASN cc_start: 0.8566 (t0) cc_final: 0.8008 (t0)
REVERT: A  728 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6626 (tp40)
REVERT: A  732 MET cc_start: 0.8921 (mmm) cc_final: 0.8686 (mmm)
REVERT: A  740 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8346 (tpp80)
REVERT: A  741 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7863 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7757 (mm-40)
REVERT: A  852 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8199 (mtm110)
REVERT: A  920 ASN cc_start: 0.8697 (p0) cc_final: 0.8348 (p0)
REVERT: A 1037 GLU cc_start: 0.8315 (mp0) cc_final: 0.7950 (mp0)
REVERT: A 1041 LYS cc_start: 0.7980 (tttm) cc_final: 0.7618 (ttmm)
REVERT: B  367 ASP cc_start: 0.6384 (m-30) cc_final: 0.5793 (m-30)
REVERT: B  386 ARG cc_start: 0.6891 (ttp-110) cc_final: 0.6553 (ttp-110)
REVERT: B  456 PHE cc_start: 0.7967 (t80) cc_final: 0.7655 (t80)
REVERT: B  466 LEU cc_start: 0.8829 (mm) cc_final: 0.8620 (mt)
REVERT: B  496 GLU cc_start: 0.8731 (tp30) cc_final: 0.7953 (tp30)
REVERT: B  499 GLN cc_start: 0.7536 (tm-30) cc_final: 0.7012 (tm-30)
REVERT: B  525 MET cc_start: 0.8103 (mmp) cc_final: 0.7709 (mmp)
REVERT: B  535 ILE cc_start: 0.8674 (pt) cc_final: 0.8360 (pp)
REVERT: B  540 ASP cc_start: 0.7950 (t0) cc_final: 0.7491 (t70)
REVERT: B  560 ASP cc_start: 0.8585 (t0) cc_final: 0.8050 (t0)
  outliers start: 35
  outliers final: 14
  residues processed: 251
  average time/residue: 0.4897
  time to fit residues: 133.5642
Evaluate side-chains
  248 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 229
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 46 optimal weight:   50.0000
   chunk 106 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 98 optimal weight:    9.9990
   chunk 119 optimal weight:   20.0000
   chunk 45 optimal weight:    0.1980
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 213 HIS
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
A 630 GLN
** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.169343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114682 restraints weight = 13872.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.83
r_work: 0.3169 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10639  Z= 0.152
  Angle     :  0.638   9.903  14352  Z= 0.317
  Chirality :  0.042   0.156   1551
  Planarity :  0.004   0.038   1848
  Dihedral  :  4.318  28.667   1385
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.48 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.62 (0.24), residues: 1252
  helix:  1.62 (0.21), residues: 595
  sheet: -1.31 (0.42), residues: 150
  loop : -0.41 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 108 
 TYR   0.019   0.001   TYR A 622 
 PHE   0.034   0.002   PHE B 355 
 TRP   0.027   0.001   TRP A 479 
 HIS   0.012   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10639)
  covalent geometry    : angle       0.63792 (14352)
  hydrogen bonds       : bond        0.03414 (  510)
  hydrogen bonds       : angle       3.92606 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 235
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8301 (p90) cc_final: 0.7824 (p90)
REVERT: A   81 GLU cc_start: 0.8101 (pp20) cc_final: 0.7366 (pp20)
REVERT: A   83 PHE cc_start: 0.7915 (m-80) cc_final: 0.7457 (m-10)
REVERT: A   85 GLU cc_start: 0.8058 (pp20) cc_final: 0.7789 (pp20)
REVERT: A  149 GLU cc_start: 0.8026 (tt0) cc_final: 0.7790 (tm-30)
REVERT: A  157 ASN cc_start: 0.7191 (t0) cc_final: 0.6846 (t0)
REVERT: A  172 GLU cc_start: 0.7210 (pp20) cc_final: 0.6964 (pp20)
REVERT: A  177 LEU cc_start: 0.8059 (tp) cc_final: 0.7611 (tm)
REVERT: A  205 GLN cc_start: 0.7542 (pt0) cc_final: 0.6981 (pp30)
REVERT: A  264 LYS cc_start: 0.8506 (ptmm) cc_final: 0.8097 (ptmm)
REVERT: A  286 MET cc_start: 0.7587 (mmp) cc_final: 0.7000 (mmp)
REVERT: A  382 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7916 (tpt-90)
REVERT: A  432 TYR cc_start: 0.9058 (p90) cc_final: 0.8694 (p90)
REVERT: A  474 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7786 (mp0)
REVERT: A  488 ASP cc_start: 0.7987 (t0) cc_final: 0.7720 (t70)
REVERT: A  494 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8042 (tm-30)
REVERT: A  677 ASN cc_start: 0.8555 (t0) cc_final: 0.7994 (t0)
REVERT: A  728 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6642 (tp40)
REVERT: A  733 LYS cc_start: 0.8866 (mttp) cc_final: 0.8563 (mtpp)
REVERT: A  740 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8334 (tpp80)
REVERT: A  741 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7888 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7707 (mm-40)
REVERT: A  852 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8199 (mtm110)
REVERT: A  920 ASN cc_start: 0.8661 (p0) cc_final: 0.8306 (p0)
REVERT: A 1010 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.6958 (mtp)
REVERT: A 1037 GLU cc_start: 0.8310 (mp0) cc_final: 0.7938 (mp0)
REVERT: A 1041 LYS cc_start: 0.7948 (tttm) cc_final: 0.7588 (ttmm)
REVERT: B  367 ASP cc_start: 0.6376 (m-30) cc_final: 0.5923 (m-30)
REVERT: B  386 ARG cc_start: 0.6902 (ttp-110) cc_final: 0.6544 (ttp-110)
REVERT: B  466 LEU cc_start: 0.8841 (mm) cc_final: 0.8612 (mt)
REVERT: B  496 GLU cc_start: 0.8737 (tp30) cc_final: 0.7950 (tp30)
REVERT: B  499 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7018 (tm-30)
REVERT: B  525 MET cc_start: 0.8081 (mmp) cc_final: 0.7692 (mmp)
REVERT: B  535 ILE cc_start: 0.8697 (pt) cc_final: 0.8374 (pp)
REVERT: B  540 ASP cc_start: 0.7942 (t0) cc_final: 0.7488 (t70)
REVERT: B  560 ASP cc_start: 0.8553 (t0) cc_final: 0.8063 (t0)
  outliers start: 30
  outliers final: 10
  residues processed: 247
  average time/residue: 0.4908
  time to fit residues: 131.6050
Evaluate side-chains
  242 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 227
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 115 optimal weight:   40.0000
   chunk 108 optimal weight:    0.0670
   chunk 17 optimal weight:    0.0270
   chunk 74 optimal weight:   10.0000
   chunk 91 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 89 optimal weight:    9.9990
   chunk 90 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    1.1780

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 213 HIS
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 495 HIS
A 630 GLN
** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 HIS
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.171261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.115710 restraints weight = 16144.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.09
r_work: 0.3181 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10639  Z= 0.127
  Angle     :  0.642  12.153  14352  Z= 0.318
  Chirality :  0.042   0.156   1551
  Planarity :  0.004   0.037   1848
  Dihedral  :  4.284  28.160   1385
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 23.86 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.66 (0.24), residues: 1252
  helix:  1.66 (0.21), residues: 597
  sheet: -1.31 (0.41), residues: 150
  loop : -0.42 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 108 
 TYR   0.019   0.001   TYR A 622 
 PHE   0.058   0.002   PHE A 734 
 TRP   0.027   0.001   TRP A 479 
 HIS   0.012   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10639)
  covalent geometry    : angle       0.64169 (14352)
  hydrogen bonds       : bond        0.03326 (  510)
  hydrogen bonds       : angle       3.92034 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 244
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8304 (p90) cc_final: 0.7827 (p90)
REVERT: A   81 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7335 (pp20)
REVERT: A   82 PHE cc_start: 0.8166 (m-10) cc_final: 0.7820 (m-10)
REVERT: A   83 PHE cc_start: 0.7901 (m-80) cc_final: 0.7472 (m-10)
REVERT: A   85 GLU cc_start: 0.8095 (pp20) cc_final: 0.7738 (tm-30)
REVERT: A  149 GLU cc_start: 0.8048 (tt0) cc_final: 0.7806 (tm-30)
REVERT: A  157 ASN cc_start: 0.7152 (t0) cc_final: 0.6819 (t0)
REVERT: A  177 LEU cc_start: 0.8100 (tp) cc_final: 0.7613 (tm)
REVERT: A  195 TRP cc_start: 0.8012 (m100) cc_final: 0.7647 (m100)
REVERT: A  205 GLN cc_start: 0.7552 (pt0) cc_final: 0.6947 (pp30)
REVERT: A  206 LYS cc_start: 0.8991 (ptpp) cc_final: 0.8768 (ptpp)
REVERT: A  264 LYS cc_start: 0.8493 (ptmm) cc_final: 0.8090 (ptmm)
REVERT: A  286 MET cc_start: 0.7649 (mmp) cc_final: 0.7269 (mmp)
REVERT: A  382 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7918 (tpt-90)
REVERT: A  432 TYR cc_start: 0.9014 (p90) cc_final: 0.8655 (p90)
REVERT: A  474 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7799 (mp0)
REVERT: A  488 ASP cc_start: 0.7897 (t0) cc_final: 0.7621 (t70)
REVERT: A  494 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8007 (tm-30)
REVERT: A  677 ASN cc_start: 0.8535 (t0) cc_final: 0.7984 (t0)
REVERT: A  728 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6404 (tp40)
REVERT: A  733 LYS cc_start: 0.8861 (mttp) cc_final: 0.8526 (mtpp)
REVERT: A  809 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7763 (mm-40)
REVERT: A  852 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8189 (mtm110)
REVERT: A  920 ASN cc_start: 0.8585 (p0) cc_final: 0.8249 (p0)
REVERT: A 1037 GLU cc_start: 0.8301 (mp0) cc_final: 0.7917 (mp0)
REVERT: A 1041 LYS cc_start: 0.8003 (tttm) cc_final: 0.7637 (ttmm)
REVERT: B  367 ASP cc_start: 0.6519 (m-30) cc_final: 0.6000 (m-30)
REVERT: B  386 ARG cc_start: 0.6907 (ttp-110) cc_final: 0.6584 (ttp-110)
REVERT: B  466 LEU cc_start: 0.8870 (mm) cc_final: 0.8636 (mt)
REVERT: B  491 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8749 (mp)
REVERT: B  496 GLU cc_start: 0.8744 (tp30) cc_final: 0.7938 (tp30)
REVERT: B  499 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7007 (tm-30)
REVERT: B  525 MET cc_start: 0.8069 (mmp) cc_final: 0.7683 (mmp)
REVERT: B  535 ILE cc_start: 0.8678 (pt) cc_final: 0.8359 (pp)
REVERT: B  540 ASP cc_start: 0.7933 (t0) cc_final: 0.7481 (t70)
REVERT: B  560 ASP cc_start: 0.8538 (t0) cc_final: 0.8061 (t0)
  outliers start: 19
  outliers final: 9
  residues processed: 253
  average time/residue: 0.5004
  time to fit residues: 137.0316
Evaluate side-chains
  245 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 231
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 35 optimal weight:    0.5980
   chunk 107 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0060
   chunk 91 optimal weight:    8.9990
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 122 optimal weight:    5.9990
   overall best weight:    1.6800

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 213 HIS
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 GLN
A 803 ASN
** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 591 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.170592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.116101 restraints weight = 14062.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.84
r_work: 0.3194 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10639  Z= 0.138
  Angle     :  0.655  11.093  14352  Z= 0.323
  Chirality :  0.042   0.176   1551
  Planarity :  0.004   0.035   1848
  Dihedral  :  4.292  27.826   1385
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 24.46 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.67 (0.24), residues: 1252
  helix:  1.65 (0.21), residues: 597
  sheet: -1.24 (0.41), residues: 149
  loop : -0.41 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 108 
 TYR   0.013   0.001   TYR B 556 
 PHE   0.032   0.002   PHE B 355 
 TRP   0.024   0.001   TRP A 479 
 HIS   0.012   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10639)
  covalent geometry    : angle       0.65454 (14352)
  hydrogen bonds       : bond        0.03359 (  510)
  hydrogen bonds       : angle       3.93190 ( 1467)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 237
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8299 (p90) cc_final: 0.7809 (p90)
REVERT: A   81 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7303 (pp20)
REVERT: A   82 PHE cc_start: 0.8048 (m-10) cc_final: 0.7797 (m-10)
REVERT: A   83 PHE cc_start: 0.7905 (m-80) cc_final: 0.7431 (m-10)
REVERT: A   85 GLU cc_start: 0.8096 (pp20) cc_final: 0.7773 (tm-30)
REVERT: A  149 GLU cc_start: 0.8010 (tt0) cc_final: 0.7789 (tm-30)
REVERT: A  157 ASN cc_start: 0.7173 (t0) cc_final: 0.6842 (t0)
REVERT: A  162 ARG cc_start: 0.8423 (mtp180) cc_final: 0.8166 (mtp85)
REVERT: A  172 GLU cc_start: 0.7138 (pp20) cc_final: 0.6838 (pp20)
REVERT: A  177 LEU cc_start: 0.8089 (tp) cc_final: 0.7628 (tm)
REVERT: A  195 TRP cc_start: 0.8003 (m100) cc_final: 0.7661 (m100)
REVERT: A  205 GLN cc_start: 0.7496 (pt0) cc_final: 0.6936 (pp30)
REVERT: A  206 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8764 (ptpp)
REVERT: A  264 LYS cc_start: 0.8501 (ptmm) cc_final: 0.8093 (ptmm)
REVERT: A  286 MET cc_start: 0.7599 (mmp) cc_final: 0.7187 (mmp)
REVERT: A  382 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7907 (tpt-90)
REVERT: A  432 TYR cc_start: 0.9018 (p90) cc_final: 0.8653 (p90)
REVERT: A  474 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7763 (mp0)
REVERT: A  488 ASP cc_start: 0.7925 (t0) cc_final: 0.7651 (t70)
REVERT: A  494 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7968 (tm-30)
REVERT: A  677 ASN cc_start: 0.8532 (t0) cc_final: 0.8014 (t0)
REVERT: A  728 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6675 (tp40)
REVERT: A  733 LYS cc_start: 0.8838 (mttp) cc_final: 0.8510 (mtpp)
REVERT: A  740 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8167 (tpp80)
REVERT: A  809 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7810 (mm-40)
REVERT: A  852 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8186 (mtm110)
REVERT: A  920 ASN cc_start: 0.8527 (p0) cc_final: 0.8199 (p0)
REVERT: A 1037 GLU cc_start: 0.8247 (mp0) cc_final: 0.7869 (mp0)
REVERT: A 1041 LYS cc_start: 0.8041 (tttm) cc_final: 0.7609 (ttmm)
REVERT: B  367 ASP cc_start: 0.6450 (m-30) cc_final: 0.6087 (m-30)
REVERT: B  386 ARG cc_start: 0.6930 (ttp-110) cc_final: 0.6717 (ttp-110)
REVERT: B  466 LEU cc_start: 0.8882 (mm) cc_final: 0.8634 (mt)
REVERT: B  491 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8759 (mp)
REVERT: B  496 GLU cc_start: 0.8753 (tp30) cc_final: 0.7941 (tp30)
REVERT: B  499 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: B  525 MET cc_start: 0.8087 (mmp) cc_final: 0.7711 (mmp)
REVERT: B  535 ILE cc_start: 0.8702 (pt) cc_final: 0.8373 (pp)
REVERT: B  540 ASP cc_start: 0.7922 (t0) cc_final: 0.7478 (t70)
REVERT: B  560 ASP cc_start: 0.8541 (t0) cc_final: 0.8065 (t0)
  outliers start: 18
  outliers final: 8
  residues processed: 245
  average time/residue: 0.5254
  time to fit residues: 140.1107
Evaluate side-chains
  238 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 225
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  478 GLN
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 3 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 47 optimal weight:    0.0040
   chunk 112 optimal weight:    8.9990
   chunk 48 optimal weight:    0.2980
   chunk 56 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   overall best weight:    2.2598

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 213 HIS
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
A 630 GLN
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.169888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.115012 restraints weight = 13852.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.84
r_work: 0.3182 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10639  Z= 0.153
  Angle     :  0.666  11.026  14352  Z= 0.330
  Chirality :  0.042   0.174   1551
  Planarity :  0.004   0.033   1848
  Dihedral  :  4.285  27.960   1385
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 24.98 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.67 (0.24), residues: 1252
  helix:  1.62 (0.21), residues: 596
  sheet: -1.21 (0.42), residues: 147
  loop : -0.38 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 108 
 TYR   0.015   0.001   TYR A 182 
 PHE   0.053   0.002   PHE A 734 
 TRP   0.023   0.001   TRP A 479 
 HIS   0.012   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10639)
  covalent geometry    : angle       0.66584 (14352)
  hydrogen bonds       : bond        0.03412 (  510)
  hydrogen bonds       : angle       3.95012 ( 1467)

===============================================================================
Job complete
usr+sys time: 4729.12 seconds
wall clock time: 81 minutes 13.47 seconds (4873.47 seconds total)