Starting phenix.real_space_refine
on Mon Jul 28 13:52:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7myn_24081/07_2025/7myn_24081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7myn_24081/07_2025/7myn_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7myn_24081/07_2025/7myn_24081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7myn_24081/07_2025/7myn_24081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7myn_24081/07_2025/7myn_24081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7myn_24081/07_2025/7myn_24081.cif"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.81, per 1000 atoms: 0.94
  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: 2.16
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  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: 1.29
  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: 4.01

  Time building geometry restraints manager: 2.67 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:             8.030
  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:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     31.440
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.690
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (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
 TRP   0.043   0.002   TRP A 195 
 HIS   0.003   0.001   HIS A 180 
 PHE   0.017   0.002   PHE A 734 
 TYR   0.024   0.001   TYR A 207 
 ARG   0.009   0.000   ARG A 382 

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

*********************** 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  : 1.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 HIS cc_start: 0.8156 (p90) cc_final: 0.7913 (p90)
REVERT: A   81 GLU cc_start: 0.7894 (pp20) cc_final: 0.7307 (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: 0.7680 (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: 1.3475
  time to fit residues: 479.4228
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  : 1.257 
-------------------------------------------------------------------------------
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 104 optimal weight:    9.9990
   chunk 93 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0980
   chunk 97 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 157 ASN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.170551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.112585 restraints weight = 14389.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.05
r_work: 0.3156 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10639  Z= 0.154
  Angle     :  0.647  10.611  14352  Z= 0.325
  Chirality :  0.043   0.148   1551
  Planarity :  0.004   0.046   1848
  Dihedral  :  4.609  45.641   1388
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.30 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.23), residues: 1252
  helix:  1.10 (0.21), residues: 594
  sheet: -1.05 (0.40), residues: 161
  loop : -0.46 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 195 
 HIS   0.004   0.001   HIS A 180 
 PHE   0.027   0.002   PHE A  83 
 TYR   0.018   0.001   TYR B 426 
 ARG   0.010   0.001   ARG A 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (  510)
  hydrogen bonds       : angle       4.11549 ( 1467)
  covalent geometry    : bond        0.00360 (10639)
  covalent geometry    : angle       0.64668 (14352)

*********************** 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
  287 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 261
  time to evaluate  : 1.612 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 GLU cc_start: 0.7911 (pp20) cc_final: 0.7004 (pp20)
REVERT: A   83 PHE cc_start: 0.8085 (m-80) cc_final: 0.7520 (m-80)
REVERT: A  111 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8360 (mtpt)
REVERT: A  130 MET cc_start: 0.8046 (tmm) cc_final: 0.7773 (pp-130)
REVERT: A  157 ASN cc_start: 0.7076 (t0) cc_final: 0.6639 (t0)
REVERT: A  162 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7980 (mtp85)
REVERT: A  205 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7110 (pp30)
REVERT: A  206 LYS cc_start: 0.8971 (ptpp) cc_final: 0.8680 (ptpp)
REVERT: A  264 LYS cc_start: 0.8358 (ptmm) cc_final: 0.8038 (ptmm)
REVERT: A  286 MET cc_start: 0.7139 (mmm) cc_final: 0.6924 (mmp)
REVERT: A  365 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8100 (pp20)
REVERT: A  393 ILE cc_start: 0.8684 (mm) cc_final: 0.8431 (mm)
REVERT: A  490 SER cc_start: 0.8744 (m) cc_final: 0.8488 (m)
REVERT: A  677 ASN cc_start: 0.8679 (t0) cc_final: 0.8086 (t0)
REVERT: A  740 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8276 (tpp80)
REVERT: A  745 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7920 (tpp)
REVERT: A  852 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7950 (ptp90)
REVERT: A 1037 GLU cc_start: 0.8128 (mp0) cc_final: 0.7838 (mp0)
REVERT: B  386 ARG cc_start: 0.6951 (ttp-110) cc_final: 0.6637 (ttp-110)
REVERT: B  452 TYR cc_start: 0.7619 (m-80) cc_final: 0.7348 (m-80)
REVERT: B  496 GLU cc_start: 0.8658 (tp30) cc_final: 0.7917 (tp30)
REVERT: B  499 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6946 (tm-30)
REVERT: B  535 ILE cc_start: 0.8616 (pt) cc_final: 0.8336 (pp)
REVERT: B  540 ASP cc_start: 0.7899 (t0) cc_final: 0.7325 (t70)
REVERT: B  560 ASP cc_start: 0.8012 (t0) cc_final: 0.7798 (t70)
  outliers start: 26
  outliers final: 7
  residues processed: 272
  average time/residue: 1.4166
  time to fit residues: 416.8150
Evaluate side-chains
  253 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 243
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
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  745 MET
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 25 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 120 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 123 optimal weight:   40.0000
   chunk 105 optimal weight:   10.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 803 ASN
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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.165797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.109517 restraints weight = 15990.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 3.03
r_work: 0.3099 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  10639  Z= 0.274
  Angle     :  0.681   9.246  14352  Z= 0.344
  Chirality :  0.045   0.140   1551
  Planarity :  0.004   0.036   1848
  Dihedral  :  4.811  53.130   1388
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1252
  helix:  1.17 (0.21), residues: 592
  sheet: -1.23 (0.40), residues: 146
  loop : -0.45 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 195 
 HIS   0.012   0.001   HIS A 213 
 PHE   0.037   0.003   PHE B 456 
 TYR   0.016   0.002   TYR A 207 
 ARG   0.006   0.001   ARG A 899 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  510)
  hydrogen bonds       : angle       4.13842 ( 1467)
  covalent geometry    : bond        0.00647 (10639)
  covalent geometry    : angle       0.68122 (14352)

*********************** 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
  288 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 251
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 GLU cc_start: 0.7722 (pp20) cc_final: 0.7356 (pp20)
REVERT: A  157 ASN cc_start: 0.7239 (t0) cc_final: 0.6873 (t0)
REVERT: A  205 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6936 (pp30)
REVERT: A  264 LYS cc_start: 0.8646 (ptmm) cc_final: 0.8230 (ptmm)
REVERT: A  286 MET cc_start: 0.7262 (mmm) cc_final: 0.7053 (mmp)
REVERT: A  365 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8141 (pp20)
REVERT: A  382 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7992 (tpt-90)
REVERT: A  393 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8777 (mm)
REVERT: A  474 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7970 (mp0)
REVERT: A  677 ASN cc_start: 0.8678 (t0) cc_final: 0.8055 (t0)
REVERT: A  728 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7508 (tm-30)
REVERT: A  740 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8374 (tpp80)
REVERT: A  809 GLN cc_start: 0.8811 (mp10) cc_final: 0.8488 (mp10)
REVERT: A 1010 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.6408 (mpt)
REVERT: B  386 ARG cc_start: 0.6977 (ttp-110) cc_final: 0.6528 (ttp-110)
REVERT: B  456 PHE cc_start: 0.8028 (t80) cc_final: 0.7813 (t80)
REVERT: B  458 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8357 (pm20)
REVERT: B  496 GLU cc_start: 0.8770 (tp30) cc_final: 0.7997 (tp30)
REVERT: B  499 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7037 (tm-30)
REVERT: B  525 MET cc_start: 0.8148 (mmp) cc_final: 0.7702 (mmp)
REVERT: B  535 ILE cc_start: 0.8692 (pt) cc_final: 0.8390 (pp)
REVERT: B  540 ASP cc_start: 0.7899 (t0) cc_final: 0.7384 (t70)
REVERT: B  560 ASP cc_start: 0.8083 (t0) cc_final: 0.7844 (t0)
  outliers start: 37
  outliers final: 10
  residues processed: 265
  average time/residue: 1.2458
  time to fit residues: 357.2399
Evaluate side-chains
  245 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 228
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
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  393 ILE
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  876 THR
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain B residue  370 LEU
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  491 ILE
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 18 optimal weight:    4.9990
   chunk 120 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   chunk 107 optimal weight:   20.0000
   chunk 110 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 106 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 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**
B 385 HIS
** 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 = 0.4000 r_free = 0.4000 target = 0.167622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.110099 restraints weight = 21232.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 3.50
r_work: 0.3100 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10639  Z= 0.164
  Angle     :  0.628   9.840  14352  Z= 0.312
  Chirality :  0.043   0.157   1551
  Planarity :  0.004   0.034   1848
  Dihedral  :  4.517  41.949   1388
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.12 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.24), residues: 1252
  helix:  1.40 (0.21), residues: 588
  sheet: -1.13 (0.41), residues: 146
  loop : -0.34 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 195 
 HIS   0.004   0.001   HIS B 385 
 PHE   0.035   0.002   PHE A  83 
 TYR   0.014   0.001   TYR B 556 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03540 (  510)
  hydrogen bonds       : angle       4.00910 ( 1467)
  covalent geometry    : bond        0.00389 (10639)
  covalent geometry    : angle       0.62762 (14352)

*********************** 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
  287 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 250
  time to evaluate  : 1.086 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.7994 (pp20) cc_final: 0.6935 (pp20)
REVERT: A   87 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7751 (ttp-110)
REVERT: A  157 ASN cc_start: 0.7255 (t0) cc_final: 0.6887 (t0)
REVERT: A  205 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7127 (pp30)
REVERT: A  264 LYS cc_start: 0.8534 (ptmm) cc_final: 0.8085 (ptmm)
REVERT: A  382 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7991 (tpt-90)
REVERT: A  393 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8669 (mm)
REVERT: A  432 TYR cc_start: 0.9097 (p90) cc_final: 0.8799 (p90)
REVERT: A  488 ASP cc_start: 0.8024 (t0) cc_final: 0.7744 (t70)
REVERT: A  677 ASN cc_start: 0.8636 (t0) cc_final: 0.8006 (t0)
REVERT: A  728 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7543 (tm-30)
REVERT: A  741 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7568 (ttp-110)
REVERT: A  825 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7803 (mp-120)
REVERT: A  852 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8041 (ptp90)
REVERT: A 1037 GLU cc_start: 0.8223 (mp0) cc_final: 0.7929 (mp0)
REVERT: B  386 ARG cc_start: 0.6859 (ttp-110) cc_final: 0.6583 (ttp-110)
REVERT: B  462 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8618 (mm-30)
REVERT: B  496 GLU cc_start: 0.8739 (tp30) cc_final: 0.7971 (tp30)
REVERT: B  499 GLN cc_start: 0.7454 (tm-30) cc_final: 0.6956 (tm-30)
REVERT: B  525 MET cc_start: 0.8168 (mmp) cc_final: 0.7731 (mmp)
REVERT: B  535 ILE cc_start: 0.8684 (pt) cc_final: 0.8376 (pp)
REVERT: B  540 ASP cc_start: 0.7927 (t0) cc_final: 0.7461 (t70)
REVERT: B  560 ASP cc_start: 0.8163 (t0) cc_final: 0.7700 (t0)
  outliers start: 37
  outliers final: 12
  residues processed: 265
  average time/residue: 1.1417
  time to fit residues: 326.7291
Evaluate side-chains
  258 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 240
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
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  205 GLN
Chi-restraints excluded: chain A residue  390 ASP
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  741 ARG
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  401 VAL
Chi-restraints excluded: chain B residue  462 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
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 119 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 101 optimal weight:    5.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 647 ASN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.168064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111615 restraints weight = 17470.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.19
r_work: 0.3128 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10639  Z= 0.160
  Angle     :  0.628  10.494  14352  Z= 0.312
  Chirality :  0.042   0.199   1551
  Planarity :  0.004   0.039   1848
  Dihedral  :  4.392  29.582   1388
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.41 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1252
  helix:  1.48 (0.21), residues: 596
  sheet: -1.14 (0.42), residues: 146
  loop : -0.39 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 195 
 HIS   0.005   0.001   HIS B 385 
 PHE   0.037   0.002   PHE B 456 
 TYR   0.014   0.001   TYR B 556 
 ARG   0.009   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  510)
  hydrogen bonds       : angle       3.96451 ( 1467)
  covalent geometry    : bond        0.00383 (10639)
  covalent geometry    : angle       0.62757 (14352)

*********************** 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
  286 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 245
  time to evaluate  : 1.103 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.7583 (pp20) cc_final: 0.7353 (pp20)
REVERT: A   83 PHE cc_start: 0.8028 (m-10) cc_final: 0.7789 (m-10)
REVERT: A   87 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7379 (ttp-110)
REVERT: A  109 GLU cc_start: 0.8453 (mp0) cc_final: 0.8145 (mp0)
REVERT: A  157 ASN cc_start: 0.7240 (t0) cc_final: 0.6872 (t0)
REVERT: A  195 TRP cc_start: 0.8073 (m100) cc_final: 0.7842 (m100)
REVERT: A  264 LYS cc_start: 0.8488 (ptmm) cc_final: 0.8142 (ptmm)
REVERT: A  286 MET cc_start: 0.7863 (mmp) cc_final: 0.7532 (mmp)
REVERT: A  382 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7856 (tpt-90)
REVERT: A  393 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8591 (mm)
REVERT: A  432 TYR cc_start: 0.9080 (p90) cc_final: 0.8706 (p90)
REVERT: A  474 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7853 (mp0)
REVERT: A  488 ASP cc_start: 0.7983 (t0) cc_final: 0.7729 (t70)
REVERT: A  677 ASN cc_start: 0.8598 (t0) cc_final: 0.7996 (t0)
REVERT: A  741 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7571 (ttp-110)
REVERT: A  852 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8138 (mtm110)
REVERT: A 1010 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.6644 (mpt)
REVERT: A 1037 GLU cc_start: 0.8267 (mp0) cc_final: 0.7920 (mp0)
REVERT: B  386 ARG cc_start: 0.6840 (ttp-110) cc_final: 0.6494 (ttp-110)
REVERT: B  496 GLU cc_start: 0.8736 (tp30) cc_final: 0.7952 (tp30)
REVERT: B  499 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6961 (tm-30)
REVERT: B  525 MET cc_start: 0.8162 (mmp) cc_final: 0.7746 (mmp)
REVERT: B  535 ILE cc_start: 0.8697 (pt) cc_final: 0.8377 (pp)
REVERT: B  540 ASP cc_start: 0.7952 (t0) cc_final: 0.7468 (t70)
REVERT: B  560 ASP cc_start: 0.8298 (t0) cc_final: 0.7761 (t0)
  outliers start: 41
  outliers final: 18
  residues processed: 264
  average time/residue: 1.1529
  time to fit residues: 328.7859
Evaluate side-chains
  256 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 234
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
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  390 ASP
Chi-restraints excluded: chain A residue  393 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  650 VAL
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1010 MET
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 62 optimal weight:    4.9990
   chunk 118 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 109 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 117 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    3.9786

-------------------------------------------------------------------------------
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 370 ASN
A 450 HIS
A 630 GLN
A 647 ASN
** 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.166481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110030 restraints weight = 17215.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 3.17
r_work: 0.3101 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10639  Z= 0.209
  Angle     :  0.651  10.087  14352  Z= 0.326
  Chirality :  0.043   0.149   1551
  Planarity :  0.004   0.042   1848
  Dihedral  :  4.373  25.891   1385
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.59 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.24), residues: 1252
  helix:  1.48 (0.21), residues: 597
  sheet: -1.41 (0.41), residues: 152
  loop : -0.43 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 195 
 HIS   0.006   0.001   HIS B 385 
 PHE   0.038   0.002   PHE B 456 
 TYR   0.022   0.001   TYR A 622 
 ARG   0.008   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  510)
  hydrogen bonds       : angle       3.99977 ( 1467)
  covalent geometry    : bond        0.00499 (10639)
  covalent geometry    : angle       0.65117 (14352)

*********************** 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
  275 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 239
  time to evaluate  : 1.201 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8452 (p90) cc_final: 0.7928 (p90)
REVERT: A   78 GLU cc_start: 0.7689 (pp20) cc_final: 0.7432 (pp20)
REVERT: A   87 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7756 (ttp-110)
REVERT: A  109 GLU cc_start: 0.8482 (mp0) cc_final: 0.8153 (mp0)
REVERT: A  157 ASN cc_start: 0.7217 (t0) cc_final: 0.6855 (t0)
REVERT: A  205 GLN cc_start: 0.7599 (pt0) cc_final: 0.6984 (pp30)
REVERT: A  264 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8147 (ptmm)
REVERT: A  286 MET cc_start: 0.7737 (mmp) cc_final: 0.7216 (mmp)
REVERT: A  382 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7929 (tpt-90)
REVERT: A  393 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: A  432 TYR cc_start: 0.9104 (p90) cc_final: 0.8757 (p90)
REVERT: A  474 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7834 (mp0)
REVERT: A  488 ASP cc_start: 0.7972 (t0) cc_final: 0.7698 (t70)
REVERT: A  677 ASN cc_start: 0.8570 (t0) cc_final: 0.7949 (t0)
REVERT: A  740 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8242 (tpp80)
REVERT: A  741 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7554 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8682 (mp10) cc_final: 0.7993 (mp10)
REVERT: A 1010 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.6858 (mpt)
REVERT: A 1037 GLU cc_start: 0.8300 (mp0) cc_final: 0.7898 (mp0)
REVERT: B  386 ARG cc_start: 0.6873 (ttp-110) cc_final: 0.6661 (ttp-110)
REVERT: B  496 GLU cc_start: 0.8788 (tp30) cc_final: 0.8014 (tp30)
REVERT: B  499 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7085 (tm-30)
REVERT: B  525 MET cc_start: 0.8195 (mmp) cc_final: 0.7764 (mmp)
REVERT: B  535 ILE cc_start: 0.8691 (pt) cc_final: 0.8367 (pp)
REVERT: B  540 ASP cc_start: 0.7989 (t0) cc_final: 0.7550 (t70)
REVERT: B  560 ASP cc_start: 0.8312 (t0) cc_final: 0.7999 (t0)
  outliers start: 36
  outliers final: 17
  residues processed: 259
  average time/residue: 1.1689
  time to fit residues: 327.4927
Evaluate side-chains
  248 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 227
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  393 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  650 VAL
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1010 MET
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 30 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 110 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 100 optimal weight:    8.9990
   chunk 70 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
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**
B 591 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.166595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.110293 restraints weight = 16450.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.08
r_work: 0.3111 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    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 = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  10639  Z= 0.203
  Angle     :  0.662  11.223  14352  Z= 0.328
  Chirality :  0.043   0.145   1551
  Planarity :  0.004   0.041   1848
  Dihedral  :  4.446  26.216   1385
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.76 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.24), residues: 1252
  helix:  1.56 (0.21), residues: 591
  sheet: -1.47 (0.40), residues: 152
  loop : -0.41 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 479 
 HIS   0.006   0.001   HIS B 385 
 PHE   0.036   0.002   PHE B 456 
 TYR   0.023   0.001   TYR A 622 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  510)
  hydrogen bonds       : angle       3.99888 ( 1467)
  covalent geometry    : bond        0.00487 (10639)
  covalent geometry    : angle       0.66182 (14352)

*********************** 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
  277 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 238
  time to evaluate  : 1.120 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8417 (p90) cc_final: 0.7920 (p90)
REVERT: A   78 GLU cc_start: 0.7696 (pp20) cc_final: 0.7445 (pp20)
REVERT: A   81 GLU cc_start: 0.8163 (pp20) cc_final: 0.7270 (pp20)
REVERT: A   82 PHE cc_start: 0.8291 (m-10) cc_final: 0.8065 (m-10)
REVERT: A   83 PHE cc_start: 0.8175 (m-80) cc_final: 0.7950 (m-10)
REVERT: A   87 ARG cc_start: 0.8054 (ttp-110) cc_final: 0.7797 (ttp-110)
REVERT: A  109 GLU cc_start: 0.8508 (mp0) cc_final: 0.8177 (mp0)
REVERT: A  149 GLU cc_start: 0.8064 (tt0) cc_final: 0.7829 (tm-30)
REVERT: A  157 ASN cc_start: 0.7220 (t0) cc_final: 0.6873 (t0)
REVERT: A  172 GLU cc_start: 0.7131 (pp20) cc_final: 0.6920 (pp20)
REVERT: A  205 GLN cc_start: 0.7647 (pt0) cc_final: 0.7053 (pp30)
REVERT: A  264 LYS cc_start: 0.8588 (ptmm) cc_final: 0.8224 (ptmm)
REVERT: A  286 MET cc_start: 0.7792 (mmp) cc_final: 0.7326 (mmp)
REVERT: A  382 ARG cc_start: 0.8244 (mmm160) cc_final: 0.7890 (tpt-90)
REVERT: A  393 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8724 (mm)
REVERT: A  474 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7832 (mp0)
REVERT: A  488 ASP cc_start: 0.7922 (t0) cc_final: 0.7608 (t70)
REVERT: A  677 ASN cc_start: 0.8563 (t0) cc_final: 0.7947 (t0)
REVERT: A  733 LYS cc_start: 0.8924 (mttp) cc_final: 0.8589 (mtpp)
REVERT: A  740 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8303 (tpp80)
REVERT: A  741 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7657 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8640 (mp10) cc_final: 0.7898 (mp10)
REVERT: A 1010 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.6925 (mpt)
REVERT: A 1037 GLU cc_start: 0.8304 (mp0) cc_final: 0.7875 (mp0)
REVERT: B  386 ARG cc_start: 0.6898 (ttp-110) cc_final: 0.6664 (ttp-110)
REVERT: B  489 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8478 (mm-30)
REVERT: B  496 GLU cc_start: 0.8789 (tp30) cc_final: 0.8013 (tp30)
REVERT: B  499 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7120 (tm-30)
REVERT: B  508 TYR cc_start: 0.7080 (t80) cc_final: 0.6642 (t80)
REVERT: B  525 MET cc_start: 0.8193 (mmp) cc_final: 0.7772 (mmp)
REVERT: B  535 ILE cc_start: 0.8708 (pt) cc_final: 0.8375 (pp)
REVERT: B  540 ASP cc_start: 0.7978 (t0) cc_final: 0.7550 (t70)
REVERT: B  560 ASP cc_start: 0.8531 (t0) cc_final: 0.8019 (t0)
  outliers start: 39
  outliers final: 17
  residues processed: 260
  average time/residue: 1.1350
  time to fit residues: 318.9573
Evaluate side-chains
  253 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 232
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  393 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  650 VAL
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1010 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 55 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 450 HIS
A 630 GLN
A 647 ASN
** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4010 r_free = 0.4010 target = 0.168285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.113800 restraints weight = 13818.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.81
r_work: 0.3158 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    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 = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10639  Z= 0.147
  Angle     :  0.645  10.715  14352  Z= 0.322
  Chirality :  0.042   0.170   1551
  Planarity :  0.004   0.038   1848
  Dihedral  :  4.384  27.509   1385
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.62 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.24), residues: 1252
  helix:  1.60 (0.21), residues: 592
  sheet: -1.37 (0.41), residues: 152
  loop : -0.37 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 479 
 HIS   0.006   0.001   HIS B 385 
 PHE   0.034   0.002   PHE B 355 
 TYR   0.015   0.001   TYR A 622 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03403 (  510)
  hydrogen bonds       : angle       3.99379 ( 1467)
  covalent geometry    : bond        0.00350 (10639)
  covalent geometry    : angle       0.64479 (14352)

*********************** 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
  275 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 241
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8359 (p90) cc_final: 0.7867 (p90)
REVERT: A   81 GLU cc_start: 0.8138 (pp20) cc_final: 0.7212 (pp20)
REVERT: A   83 PHE cc_start: 0.8161 (m-80) cc_final: 0.7920 (m-10)
REVERT: A   87 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7789 (ttp-110)
REVERT: A  138 ASP cc_start: 0.8821 (m-30) cc_final: 0.8574 (m-30)
REVERT: A  149 GLU cc_start: 0.8029 (tt0) cc_final: 0.7797 (tm-30)
REVERT: A  157 ASN cc_start: 0.7187 (t0) cc_final: 0.6858 (t0)
REVERT: A  177 LEU cc_start: 0.8081 (tp) cc_final: 0.7623 (tm)
REVERT: A  205 GLN cc_start: 0.7621 (pt0) cc_final: 0.7068 (pp30)
REVERT: A  264 LYS cc_start: 0.8543 (ptmm) cc_final: 0.8190 (ptmm)
REVERT: A  278 MET cc_start: 0.7553 (mmt) cc_final: 0.7106 (mmp)
REVERT: A  286 MET cc_start: 0.7710 (mmp) cc_final: 0.7218 (mmp)
REVERT: A  382 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7907 (tpt-90)
REVERT: A  432 TYR cc_start: 0.8973 (p90) cc_final: 0.8674 (p90)
REVERT: A  474 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7723 (mp0)
REVERT: A  488 ASP cc_start: 0.7931 (t0) cc_final: 0.7671 (t70)
REVERT: A  677 ASN cc_start: 0.8556 (t0) cc_final: 0.7966 (t0)
REVERT: A  733 LYS cc_start: 0.8921 (mttp) cc_final: 0.8595 (mtpp)
REVERT: A  740 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8326 (tpp80)
REVERT: A  741 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7570 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8536 (mp10) cc_final: 0.7804 (mp10)
REVERT: A 1037 GLU cc_start: 0.8289 (mp0) cc_final: 0.7841 (mp0)
REVERT: A 1041 LYS cc_start: 0.7948 (tttm) cc_final: 0.7581 (ttmm)
REVERT: B  386 ARG cc_start: 0.6889 (ttp-110) cc_final: 0.6547 (ttp-110)
REVERT: B  425 LEU cc_start: 0.8607 (mt) cc_final: 0.8390 (mp)
REVERT: B  489 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8467 (mm-30)
REVERT: B  496 GLU cc_start: 0.8779 (tp30) cc_final: 0.7982 (tp30)
REVERT: B  499 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: B  525 MET cc_start: 0.8203 (mmp) cc_final: 0.7800 (mmp)
REVERT: B  535 ILE cc_start: 0.8720 (pt) cc_final: 0.8385 (pp)
REVERT: B  540 ASP cc_start: 0.7958 (t0) cc_final: 0.7546 (t70)
REVERT: B  560 ASP cc_start: 0.8520 (t0) cc_final: 0.7977 (t0)
  outliers start: 34
  outliers final: 13
  residues processed: 255
  average time/residue: 1.1934
  time to fit residues: 327.8337
Evaluate side-chains
  241 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 226
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   85 GLU
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  629 SER
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  741 ARG
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 70 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 113 optimal weight:   10.0000
   chunk 106 optimal weight:   20.0000
   chunk 0 optimal weight:   50.0000
   chunk 1 optimal weight:   50.0000
   chunk 9 optimal weight:    6.9990
   overall best weight:    4.1588

-------------------------------------------------------------------------------
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 370 ASN
A 450 HIS
A 630 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 = 0.3989 r_free = 0.3989 target = 0.166525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110431 restraints weight = 15841.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.01
r_work: 0.3111 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    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 = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10639  Z= 0.220
  Angle     :  0.696  10.492  14352  Z= 0.349
  Chirality :  0.044   0.196   1551
  Planarity :  0.004   0.036   1848
  Dihedral  :  4.486  27.012   1385
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.17 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.24), residues: 1252
  helix:  1.50 (0.21), residues: 588
  sheet: -1.41 (0.40), residues: 152
  loop : -0.43 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 195 
 HIS   0.010   0.001   HIS A 213 
 PHE   0.031   0.002   PHE B 355 
 TYR   0.015   0.001   TYR B 556 
 ARG   0.007   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  510)
  hydrogen bonds       : angle       4.07625 ( 1467)
  covalent geometry    : bond        0.00526 (10639)
  covalent geometry    : angle       0.69624 (14352)

*********************** 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
  257 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 2.540 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8412 (p90) cc_final: 0.7911 (p90)
REVERT: A   81 GLU cc_start: 0.8090 (pp20) cc_final: 0.7116 (pp20)
REVERT: A   82 PHE cc_start: 0.8300 (m-10) cc_final: 0.8088 (m-10)
REVERT: A   83 PHE cc_start: 0.8128 (m-80) cc_final: 0.7925 (m-10)
REVERT: A   87 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7687 (ttp-110)
REVERT: A  149 GLU cc_start: 0.8044 (tt0) cc_final: 0.7808 (tm-30)
REVERT: A  157 ASN cc_start: 0.7230 (t0) cc_final: 0.6887 (t0)
REVERT: A  177 LEU cc_start: 0.8117 (tp) cc_final: 0.7641 (tm)
REVERT: A  205 GLN cc_start: 0.7572 (pt0) cc_final: 0.6871 (pp30)
REVERT: A  206 LYS cc_start: 0.9083 (ptpp) cc_final: 0.8767 (ptpp)
REVERT: A  264 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8314 (ptmm)
REVERT: A  278 MET cc_start: 0.7647 (mmt) cc_final: 0.7246 (mmp)
REVERT: A  286 MET cc_start: 0.7768 (mmp) cc_final: 0.7205 (mmp)
REVERT: A  382 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7941 (tpt-90)
REVERT: A  474 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7804 (mp0)
REVERT: A  488 ASP cc_start: 0.7931 (t0) cc_final: 0.7605 (t70)
REVERT: A  677 ASN cc_start: 0.8555 (t0) cc_final: 0.7933 (t0)
REVERT: A  732 MET cc_start: 0.8713 (tpp) cc_final: 0.8486 (mmm)
REVERT: A  733 LYS cc_start: 0.8915 (mttp) cc_final: 0.8598 (mtpp)
REVERT: A  740 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8359 (tpp80)
REVERT: A  741 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7537 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8638 (mp10) cc_final: 0.7916 (mp10)
REVERT: A  825 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7673 (mp-120)
REVERT: A 1037 GLU cc_start: 0.8318 (mp0) cc_final: 0.7954 (mp0)
REVERT: A 1041 LYS cc_start: 0.8009 (tttm) cc_final: 0.7670 (ttmm)
REVERT: B  330 ASP cc_start: 0.8313 (p0) cc_final: 0.7402 (p0)
REVERT: B  386 ARG cc_start: 0.6905 (ttp-110) cc_final: 0.6574 (ttp-110)
REVERT: B  425 LEU cc_start: 0.8591 (mt) cc_final: 0.8351 (mp)
REVERT: B  496 GLU cc_start: 0.8813 (tp30) cc_final: 0.8039 (tp30)
REVERT: B  499 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7128 (tm-30)
REVERT: B  525 MET cc_start: 0.8227 (mmp) cc_final: 0.7757 (mmp)
REVERT: B  535 ILE cc_start: 0.8726 (pt) cc_final: 0.8379 (pp)
REVERT: B  540 ASP cc_start: 0.7992 (t0) cc_final: 0.7599 (t70)
REVERT: B  560 ASP cc_start: 0.8575 (t0) cc_final: 0.8066 (t0)
  outliers start: 24
  outliers final: 14
  residues processed: 247
  average time/residue: 1.9232
  time to fit residues: 513.4147
Evaluate side-chains
  242 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 225
  time to evaluate  : 2.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   85 GLU
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  629 SER
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  974 THR
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  539 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 45 optimal weight:    6.9990
   chunk 46 optimal weight:   40.0000
   chunk 102 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0370
   chunk 91 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0980
   chunk 18 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   overall best weight:    3.4264

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.166895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.111159 restraints weight = 15502.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.98
r_work: 0.3124 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    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 = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10639  Z= 0.192
  Angle     :  0.685  10.328  14352  Z= 0.344
  Chirality :  0.044   0.183   1551
  Planarity :  0.004   0.035   1848
  Dihedral  :  4.482  27.758   1385
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.69 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.24), residues: 1252
  helix:  1.48 (0.21), residues: 589
  sheet: -1.39 (0.40), residues: 151
  loop : -0.46 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 479 
 HIS   0.007   0.001   HIS B 385 
 PHE   0.031   0.002   PHE B 355 
 TYR   0.017   0.001   TYR A 182 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  510)
  hydrogen bonds       : angle       4.06432 ( 1467)
  covalent geometry    : bond        0.00460 (10639)
  covalent geometry    : angle       0.68477 (14352)

********************** 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
  258 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 235
  time to evaluate  : 1.218 
Fit side-chains
REVERT: A   59 HIS cc_start: 0.8314 (p90) cc_final: 0.7794 (p90)
REVERT: A   81 GLU cc_start: 0.8072 (pp20) cc_final: 0.7061 (pp20)
REVERT: A   82 PHE cc_start: 0.8287 (m-10) cc_final: 0.8080 (m-10)
REVERT: A   83 PHE cc_start: 0.8118 (m-80) cc_final: 0.7882 (m-10)
REVERT: A   87 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7698 (ttp-110)
REVERT: A  149 GLU cc_start: 0.8049 (tt0) cc_final: 0.7818 (tm-30)
REVERT: A  157 ASN cc_start: 0.7227 (t0) cc_final: 0.6888 (t0)
REVERT: A  177 LEU cc_start: 0.8107 (tp) cc_final: 0.7638 (tm)
REVERT: A  205 GLN cc_start: 0.7640 (pt0) cc_final: 0.6912 (pp30)
REVERT: A  206 LYS cc_start: 0.9089 (ptpp) cc_final: 0.8809 (ptpp)
REVERT: A  264 LYS cc_start: 0.8657 (ptmm) cc_final: 0.8309 (ptmm)
REVERT: A  278 MET cc_start: 0.7648 (mmt) cc_final: 0.7342 (mmp)
REVERT: A  286 MET cc_start: 0.7760 (mmp) cc_final: 0.7190 (mmp)
REVERT: A  382 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7939 (tpt-90)
REVERT: A  393 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8715 (mm)
REVERT: A  432 TYR cc_start: 0.9005 (p90) cc_final: 0.8690 (p90)
REVERT: A  474 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7818 (mp0)
REVERT: A  488 ASP cc_start: 0.7938 (t0) cc_final: 0.7664 (t70)
REVERT: A  677 ASN cc_start: 0.8547 (t0) cc_final: 0.7942 (t0)
REVERT: A  728 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6619 (tp40)
REVERT: A  732 MET cc_start: 0.8746 (tpp) cc_final: 0.8495 (mmm)
REVERT: A  733 LYS cc_start: 0.8904 (mttp) cc_final: 0.8608 (mtpp)
REVERT: A  741 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7648 (ttp-110)
REVERT: A  809 GLN cc_start: 0.8563 (mp10) cc_final: 0.7829 (mp10)
REVERT: A  825 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7657 (mp-120)
REVERT: A 1037 GLU cc_start: 0.8311 (mp0) cc_final: 0.7939 (mp0)
REVERT: A 1041 LYS cc_start: 0.7974 (tttm) cc_final: 0.7628 (ttmm)
REVERT: B  386 ARG cc_start: 0.6922 (ttp-110) cc_final: 0.6578 (ttp-110)
REVERT: B  496 GLU cc_start: 0.8807 (tp30) cc_final: 0.8017 (tp30)
REVERT: B  499 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7131 (tm-30)
REVERT: B  525 MET cc_start: 0.8231 (mmp) cc_final: 0.7780 (mmp)
REVERT: B  535 ILE cc_start: 0.8739 (pt) cc_final: 0.8387 (pp)
REVERT: B  540 ASP cc_start: 0.7985 (t0) cc_final: 0.7599 (t70)
REVERT: B  560 ASP cc_start: 0.8521 (t0) cc_final: 0.8112 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 250
  average time/residue: 1.2435
  time to fit residues: 336.4049
Evaluate side-chains
  247 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 229
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  393 ILE
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  674 GLU
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  974 THR
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  539 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 109 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 15 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 106 optimal weight:    9.9990
   chunk 78 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 HIS
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 564 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.168491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.112419 restraints weight = 17684.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.17
r_work: 0.3130 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10639  Z= 0.161
  Angle     :  0.688  10.652  14352  Z= 0.345
  Chirality :  0.043   0.163   1551
  Planarity :  0.004   0.035   1848
  Dihedral  :  4.454  27.217   1385
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 24.46 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1252
  helix:  1.51 (0.21), residues: 589
  sheet: -1.42 (0.41), residues: 150
  loop : -0.40 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 479 
 HIS   0.011   0.001   HIS A 213 
 PHE   0.075   0.002   PHE A 734 
 TYR   0.024   0.001   TYR A 622 
 ARG   0.007   0.001   ARG B 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03532 (  510)
  hydrogen bonds       : angle       4.06647 ( 1467)
  covalent geometry    : bond        0.00386 (10639)
  covalent geometry    : angle       0.68751 (14352)

===============================================================================
Job complete
usr+sys time: 10505.34 seconds
wall clock time: 184 minutes 12.62 seconds (11052.62 seconds total)