Starting phenix.real_space_refine
on Mon Jul 28 19:30:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dcp_27327/07_2025/8dcp_27327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dcp_27327/07_2025/8dcp_27327.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dcp_27327/07_2025/8dcp_27327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dcp_27327/07_2025/8dcp_27327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dcp_27327/07_2025/8dcp_27327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dcp_27327/07_2025/8dcp_27327.cif"
  }
  resolution = 2.41
  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=   1.000
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      75      5.16       5
     C    6724      2.51       5
     N    1835      2.21       5
     O    1961      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10595
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8233
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1005, 8222
          Classifications: {'peptide': 1005}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 1005, 8222
          Classifications: {'peptide': 1005}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 8389
    Chain: "B"
      Number of atoms: 2341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2341
          Classifications: {'peptide': 276}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 271}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 20
          Classifications: {'water': 20}
          Link IDs: {None: 19}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 704 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 704 " occ=0.50
  Time building chain proxies: 9.96, per 1000 atoms: 0.94
  Number of scatterers: 10595
  At special positions: 0
  Unit cell: (89.88, 130.54, 119.84, 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      75     16.00
     O    1961      8.00
     N    1835      7.00
     C    6724      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: 2.59
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2454

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 11 sheets defined
      52.1% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 52
    Processing helix  chain 'A' and resid 64 through 68
      removed outlier: 3.705A  pdb=" N   SER A  67 " --> pdb=" O   ASP A  64 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR A  68 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 64 through 68'
    Processing helix  chain 'A' and resid 89 through 93
      removed outlier: 3.564A  pdb=" N   LEU A  92 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG A  93 " --> pdb=" O   CYS A  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 89 through 93'
    Processing helix  chain 'A' and resid 107 through 122
      removed outlier: 3.509A  pdb=" N   LYS A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.684A  pdb=" N   ASP A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 155
      removed outlier: 4.309A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 4.394A  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
      removed outlier: 3.544A  pdb=" N   ASN A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 232
      removed outlier: 3.866A  pdb=" N   SER A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
    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 296
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.538A  pdb=" N   SER A 308 " --> pdb=" O   PRO A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 496
    Processing helix  chain 'A' and resid 498 through 503
      removed outlier: 3.683A  pdb=" N   ARG A 502 " --> pdb=" O   TRP A 498 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 498 through 503'
    Processing helix  chain 'A' and resid 524 through 536
      removed outlier: 3.517A  pdb=" N   GLN A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 557 through 563
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 571
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 4.045A  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 623
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 639 through 642
    Processing helix  chain 'A' and resid 647 through 660
    Processing helix  chain 'A' and resid 660 through 674
      removed outlier: 3.690A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLU A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 722
      removed outlier: 4.058A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 739
    Processing helix  chain 'A' and resid 741 through 748
    Processing helix  chain 'A' and resid 765 through 769
    Processing helix  chain 'A' and resid 789 through 794
      removed outlier: 4.330A  pdb=" N   LEU A 793 " --> pdb=" O   MET A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 857 through 864
    Processing helix  chain 'A' and resid 871 through 874
    Processing helix  chain 'A' and resid 875 through 885
    Processing helix  chain 'A' and resid 888 through 912
      removed outlier: 4.245A  pdb=" N   ALA A 892 " --> pdb=" O   GLU A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.541A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 993
    Processing helix  chain 'A' and resid 994 through 1004
      removed outlier: 3.787A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1026
      removed outlier: 3.889A  pdb=" N   ILE A1019 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   TYR A1021 " --> pdb=" O   ASP A1017 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ILE A1022 " --> pdb=" O   ASP A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1048
      removed outlier: 3.561A  pdb=" N   ALA A1046 " --> pdb=" O   GLN A1042 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 347
    Processing helix  chain 'B' and resid 400 through 411
      removed outlier: 3.815A  pdb=" N   LEU B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 416
      removed outlier: 3.550A  pdb=" N   GLN B 415 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 509
      removed outlier: 3.858A  pdb=" N   LYS B 506 " --> pdb=" O   GLU B 502 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   GLU B 507 " --> pdb=" O   ARG B 503 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   TYR B 508 " --> pdb=" O   TYR B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 514
      removed outlier: 3.863A  pdb=" N   LYS B 513 " --> pdb=" O   GLU B 510 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ARG B 514 " --> pdb=" O   LYS B 511 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 510 through 514'
    Processing helix  chain 'B' and resid 517 through 588
      removed outlier: 4.136A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B 527 " --> pdb=" O   ARG B 523 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR B 528 " --> pdb=" O   ILE B 524 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
      removed outlier: 3.999A  pdb=" N   GLY B 588 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 596
      removed outlier: 4.054A  pdb=" N   LEU B 594 " --> pdb=" O   ARG B 590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35
      removed outlier: 3.601A  pdb=" N   VAL A  22 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLU A  23 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   VAL A 101 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   LEU A  25 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   PHE A  70 " --> pdb=" O   PHE A  82 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER A  72 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212
      removed outlier: 4.457A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326
      removed outlier: 6.751A  pdb=" N   LYS A 325 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.788A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372
      removed outlier: 3.794A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752
    Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771
      removed outlier: 6.924A  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 377 through 382
      removed outlier: 4.434A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386

    521 hydrogen bonds defined for protein.
    1492 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: 3.93

  Time building geometry restraints manager: 3.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3480
        1.34 -     1.46: 2355
        1.46 -     1.58: 4841
        1.58 -     1.70: 0
        1.70 -     1.82: 117
  Bond restraints: 10793
  Sorted by residual:
  bond pdb=" CG1 ILE A 121 "
       pdb=" CD1 ILE A 121 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.07e+00
  bond pdb=" CG1 ILE A 894 "
       pdb=" CD1 ILE A 894 "
    ideal  model  delta    sigma   weight residual
    1.513  1.450  0.063 3.90e-02 6.57e+02 2.58e+00
  bond pdb=" CG  LYS A 132 "
       pdb=" CD  LYS A 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.02e+00
  bond pdb=" CB  LYS A 132 "
       pdb=" CG  LYS A 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.75e+00
  bond pdb=" CB  MET B 322 "
       pdb=" CG  MET B 322 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.70e+00
  ... (remaining 10788 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 14311
        2.09 -     4.17: 188
        4.17 -     6.26: 30
        6.26 -     8.35: 13
        8.35 -    10.44: 6
  Bond angle restraints: 14548
  Sorted by residual:
  angle pdb=" CB  LYS A 132 "
        pdb=" CG  LYS A 132 "
        pdb=" CD  LYS A 132 "
      ideal   model   delta    sigma   weight residual
     111.30  121.47  -10.17 2.30e+00 1.89e-01 1.96e+01
  angle pdb=" CA  MET B 322 "
        pdb=" CB  MET B 322 "
        pdb=" CG  MET B 322 "
      ideal   model   delta    sigma   weight residual
     114.10  122.17   -8.07 2.00e+00 2.50e-01 1.63e+01
  angle pdb=" CB  MET B 563 "
        pdb=" CG  MET B 563 "
        pdb=" SD  MET B 563 "
      ideal   model   delta    sigma   weight residual
     112.70  102.26   10.44 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" CB  MET A 299 "
        pdb=" CG  MET A 299 "
        pdb=" SD  MET A 299 "
      ideal   model   delta    sigma   weight residual
     112.70  123.07  -10.37 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" CA  GLU A 493 "
        pdb=" CB  GLU A 493 "
        pdb=" CG  GLU A 493 "
      ideal   model   delta    sigma   weight residual
     114.10  120.77   -6.67 2.00e+00 2.50e-01 1.11e+01
  ... (remaining 14543 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 5413
       17.83 -    35.66: 823
       35.66 -    53.48: 284
       53.48 -    71.31: 63
       71.31 -    89.14: 29
  Dihedral angle restraints: 6612
    sinusoidal: 2829
      harmonic: 3783
  Sorted by residual:
  dihedral pdb=" CA  PRO A 200 "
           pdb=" C   PRO A 200 "
           pdb=" N   ASN A 201 "
           pdb=" CA  ASN A 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.75   18.25     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  HIS A 940 "
           pdb=" C   HIS A 940 "
           pdb=" N   LYS A 941 "
           pdb=" CA  LYS A 941 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  SER A 199 "
           pdb=" C   SER A 199 "
           pdb=" N   PRO A 200 "
           pdb=" CA  PRO A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 6609 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 971
       0.031 -    0.061: 392
       0.061 -    0.092: 128
       0.092 -    0.123: 71
       0.123 -    0.154: 8
  Chirality restraints: 1570
  Sorted by residual:
  chirality pdb=" CB  ILE A 197 "
            pdb=" CA  ILE A 197 "
            pdb=" CG1 ILE A 197 "
            pdb=" CG2 ILE A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  ILE A 191 "
            pdb=" N   ILE A 191 "
            pdb=" C   ILE A 191 "
            pdb=" CB  ILE A 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  chirality pdb=" CA  ILE A 561 "
            pdb=" N   ILE A 561 "
            pdb=" C   ILE A 561 "
            pdb=" CB  ILE A 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1567 not shown)

  Planarity restraints: 1871
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 282 "    0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO A 283 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 420 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.14e+00
        pdb=" N   PRO A 421 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 421 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 421 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 216 "   -0.022 5.00e-02 4.00e+02   3.28e-02 1.73e+00
        pdb=" N   PRO A 217 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1868 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2293
        2.78 -     3.31: 9871
        3.31 -     3.84: 18197
        3.84 -     4.37: 20893
        4.37 -     4.90: 35063
  Nonbonded interactions: 86317
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 884 "
            pdb=" OD1 ASP A 925 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   GLY B 321 "
            pdb=" ND2 ASN B 323 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" N   ASN B 319 "
            pdb=" ND2 ASN B 319 "
     model   vdw
     2.293 3.200
  nonbonded pdb=" ND2 ASN A 782 "
            pdb=" OD1 ASN A 796 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NH2 ARG A 398 "
            pdb=" OD1 ASP A 434 "
     model   vdw
     2.296 3.120
  ... (remaining 86312 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=0.50 max=1.00 mean=1.00
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:             45.840
  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:          4.570
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     32.170
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.070
  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:14.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   97.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
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   0.068  10793  Z= 0.133
  Angle     :  0.641  10.437  14548  Z= 0.317
  Chirality :  0.041   0.154   1570
  Planarity :  0.004   0.047   1871
  Dihedral  : 20.067  89.140   4158
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 33.73 %
    Favored  : 63.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.79 (0.24), residues: 1270
  helix:  1.62 (0.22), residues: 575
  sheet: -0.03 (0.42), residues: 162
  loop : -0.47 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A1047 
 PHE   0.021   0.002   PHE A 744 
 TYR   0.017   0.001   TYR B 470 
 ARG   0.011   0.000   ARG B 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15001 (  521)
  hydrogen bonds       : angle       5.56483 ( 1492)
  covalent geometry    : bond        0.00311 (10793)
  covalent geometry    : angle       0.64110 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 239
  time to evaluate  : 1.126 
Fit side-chains
REVERT: A  347 ASN cc_start: 0.7096 (t0) cc_final: 0.6637 (t0)
REVERT: A 1041 LYS cc_start: 0.7197 (tttm) cc_final: 0.6896 (tppp)
REVERT: B  326 MET cc_start: 0.5247 (mpp) cc_final: 0.4113 (ttp)
  outliers start: 35
  outliers final: 30
  residues processed: 272
  average time/residue: 1.3804
  time to fit residues: 401.8039
Evaluate side-chains
  259 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 229
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  573 LYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  782 ASN
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  942 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain B residue  330 ASP
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  533 SER
Chi-restraints excluded: chain B residue  576 THR
Chi-restraints excluded: chain B residue  578 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 64 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 115 optimal weight:    9.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
B 323 ASN
B 552 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.189690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.150094 restraints weight = 16124.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.01
r_work: 0.3495 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10793  Z= 0.121
  Angle     :  0.561   8.785  14548  Z= 0.286
  Chirality :  0.041   0.152   1570
  Planarity :  0.004   0.037   1871
  Dihedral  :  7.341  59.335   1465
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 29.99 %
    Favored  : 64.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.24), residues: 1270
  helix:  1.84 (0.22), residues: 590
  sheet: -0.03 (0.40), residues: 162
  loop : -0.43 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A  59 
 PHE   0.021   0.001   PHE A 744 
 TYR   0.017   0.001   TYR B 470 
 ARG   0.008   0.000   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  521)
  hydrogen bonds       : angle       4.35725 ( 1492)
  covalent geometry    : bond        0.00276 (10793)
  covalent geometry    : angle       0.56101 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 251
  time to evaluate  : 1.099 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.7648 (t0) cc_final: 0.7420 (t0)
REVERT: A  278 MET cc_start: 0.7491 (mmm) cc_final: 0.7096 (mpp)
REVERT: A  739 MET cc_start: 0.8050 (mtt) cc_final: 0.7605 (mtt)
REVERT: A  772 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.6336 (mtp)
REVERT: A  843 ASP cc_start: 0.8174 (t70) cc_final: 0.7969 (t70)
REVERT: A  861 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7774 (mt0)
REVERT: A 1041 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7098 (tppp)
REVERT: B  326 MET cc_start: 0.5327 (mpp) cc_final: 0.3958 (ttp)
REVERT: B  364 MET cc_start: 0.6736 (mpt) cc_final: 0.6038 (mpt)
REVERT: B  469 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6673 (tp30)
REVERT: B  532 LYS cc_start: 0.5559 (OUTLIER) cc_final: 0.5212 (mmmm)
REVERT: B  542 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6021 (ttm170)
  outliers start: 67
  outliers final: 27
  residues processed: 289
  average time/residue: 1.3079
  time to fit residues: 403.7798
Evaluate side-chains
  269 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 236
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  942 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 113 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 121 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
A  59 HIS
A 822 ASN
A 826 ASN
A 958 GLN
A1047 HIS
B 319 ASN
B 488 ASN
** B 552 GLN ** 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 = 0.4073 r_free = 0.4073 target = 0.187768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.146197 restraints weight = 20016.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.34
r_work: 0.3462 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.0901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  10793  Z= 0.157
  Angle     :  0.589   8.303  14548  Z= 0.298
  Chirality :  0.042   0.156   1570
  Planarity :  0.004   0.053   1871
  Dihedral  :  6.648  59.342   1445
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 31.35 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.97 (0.24), residues: 1270
  helix:  1.79 (0.21), residues: 598
  sheet: -0.03 (0.40), residues: 162
  loop : -0.47 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 552 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.017   0.002   PHE A 128 
 TYR   0.022   0.001   TYR B 470 
 ARG   0.009   0.000   ARG A  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04966 (  521)
  hydrogen bonds       : angle       4.25271 ( 1492)
  covalent geometry    : bond        0.00375 (10793)
  covalent geometry    : angle       0.58905 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 240
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8454 (ptm) cc_final: 0.8120 (ptt)
REVERT: A  172 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7342 (mt-10)
REVERT: A  211 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8405 (pp)
REVERT: A  347 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.6966 (t0)
REVERT: A  741 ARG cc_start: 0.7014 (mpp-170) cc_final: 0.6737 (mpp-170)
REVERT: A  772 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.6459 (mtp)
REVERT: A  857 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8453 (mp)
REVERT: A  861 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7812 (mt0)
REVERT: A 1041 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7150 (tppp)
REVERT: B  326 MET cc_start: 0.5376 (mpp) cc_final: 0.3868 (ttp)
REVERT: B  364 MET cc_start: 0.6696 (mpt) cc_final: 0.5837 (mpt)
REVERT: B  469 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6679 (tp30)
REVERT: B  532 LYS cc_start: 0.5631 (OUTLIER) cc_final: 0.5256 (mmmm)
REVERT: B  542 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.5875 (ttm170)
  outliers start: 58
  outliers final: 27
  residues processed: 270
  average time/residue: 1.3646
  time to fit residues: 393.9646
Evaluate side-chains
  270 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 233
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 100 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 114 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 107 ASN
A 384 ASN
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
B 552 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.185873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.143841 restraints weight = 26691.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 3.09
r_work: 0.3399 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10793  Z= 0.183
  Angle     :  0.622  11.693  14548  Z= 0.313
  Chirality :  0.044   0.158   1570
  Planarity :  0.004   0.056   1871
  Dihedral  :  5.973  57.791   1427
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 30.84 %
    Favored  : 63.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.91 (0.24), residues: 1270
  helix:  1.71 (0.21), residues: 598
  sheet: -0.05 (0.40), residues: 160
  loop : -0.46 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 479 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.013   0.002   PHE A 128 
 TYR   0.023   0.002   TYR B 470 
 ARG   0.009   0.001   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05162 (  521)
  hydrogen bonds       : angle       4.28667 ( 1492)
  covalent geometry    : bond        0.00440 (10793)
  covalent geometry    : angle       0.62200 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 237
  time to evaluate  : 1.129 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8582 (ptm) cc_final: 0.8309 (ptm)
REVERT: A  172 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7407 (mt-10)
REVERT: A  211 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8481 (pp)
REVERT: A  263 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7818 (mm-30)
REVERT: A  297 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7700 (pp)
REVERT: A  347 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7005 (t0)
REVERT: A  772 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6835 (mtp)
REVERT: A  777 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.4658 (mpt90)
REVERT: A  857 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8595 (mp)
REVERT: A  861 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7888 (mt0)
REVERT: B  326 MET cc_start: 0.5442 (mpp) cc_final: 0.3815 (ttp)
REVERT: B  364 MET cc_start: 0.6771 (mpt) cc_final: 0.5846 (mpt)
REVERT: B  469 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6757 (tp30)
REVERT: B  478 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7134 (tp-100)
REVERT: B  542 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.5881 (ttm170)
REVERT: B  562 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7259 (mtp180)
  outliers start: 69
  outliers final: 28
  residues processed: 273
  average time/residue: 1.3588
  time to fit residues: 396.8202
Evaluate side-chains
  274 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 235
  time to evaluate  : 1.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0010
   chunk 78 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    2.3992

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 822 ASN
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
** B 552 GLN ** 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 = 0.4060 r_free = 0.4060 target = 0.186821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.146118 restraints weight = 20302.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.46
r_work: 0.3445 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3312
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3312
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10793  Z= 0.148
  Angle     :  0.597  10.814  14548  Z= 0.299
  Chirality :  0.042   0.157   1570
  Planarity :  0.004   0.043   1871
  Dihedral  :  5.878  58.520   1427
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 30.25 %
    Favored  : 63.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.96 (0.24), residues: 1270
  helix:  1.77 (0.21), residues: 599
  sheet: -0.02 (0.39), residues: 162
  loop : -0.46 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.013   0.002   PHE A 937 
 TYR   0.019   0.001   TYR B 470 
 ARG   0.006   0.000   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04782 (  521)
  hydrogen bonds       : angle       4.19268 ( 1492)
  covalent geometry    : bond        0.00352 (10793)
  covalent geometry    : angle       0.59656 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 243
  time to evaluate  : 1.282 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7344 (mt-10)
REVERT: A  211 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8474 (pp)
REVERT: A  263 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7719 (mm-30)
REVERT: A  347 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.6964 (t0)
REVERT: A  772 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6652 (mtp)
REVERT: A  777 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.4589 (mpt90)
REVERT: A  857 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8525 (mp)
REVERT: A  861 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7853 (mt0)
REVERT: A  941 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6310 (ptpt)
REVERT: A  975 ARG cc_start: 0.7240 (mmp80) cc_final: 0.6969 (mmp80)
REVERT: A 1041 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7148 (tppp)
REVERT: B  364 MET cc_start: 0.6678 (mpt) cc_final: 0.5787 (mpt)
REVERT: B  433 GLN cc_start: 0.5735 (OUTLIER) cc_final: 0.5483 (mt0)
REVERT: B  469 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6692 (tp30)
REVERT: B  478 GLN cc_start: 0.7498 (tp-100) cc_final: 0.7072 (tp40)
REVERT: B  532 LYS cc_start: 0.5654 (OUTLIER) cc_final: 0.5274 (mmmm)
REVERT: B  542 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.5907 (ttm170)
REVERT: B  562 ARG cc_start: 0.7451 (mtp-110) cc_final: 0.7170 (mtp180)
REVERT: B  575 LYS cc_start: 0.6956 (ttmt) cc_final: 0.6598 (ptmm)
  outliers start: 72
  outliers final: 33
  residues processed: 283
  average time/residue: 1.3622
  time to fit residues: 412.7441
Evaluate side-chains
  283 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 236
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  550 LYS
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 34 optimal weight:    0.0980
   chunk 4 optimal weight:   20.0000
   chunk 103 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 117 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 107 ASN
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.186284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.147873 restraints weight = 15847.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 1.84
r_work: 0.3446 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3307
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3307
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  10793  Z= 0.164
  Angle     :  0.625  10.865  14548  Z= 0.311
  Chirality :  0.043   0.184   1570
  Planarity :  0.004   0.056   1871
  Dihedral  :  5.913  58.718   1427
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 30.76 %
    Favored  : 63.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.91 (0.24), residues: 1270
  helix:  1.73 (0.21), residues: 599
  sheet: -0.04 (0.39), residues: 162
  loop : -0.48 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.012   0.002   PHE A 667 
 TYR   0.025   0.002   TYR A 622 
 ARG   0.011   0.000   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04939 (  521)
  hydrogen bonds       : angle       4.22599 ( 1492)
  covalent geometry    : bond        0.00392 (10793)
  covalent geometry    : angle       0.62545 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 238
  time to evaluate  : 1.300 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7377 (mt-10)
REVERT: A  211 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8472 (pp)
REVERT: A  263 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7734 (mm-30)
REVERT: A  772 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.6692 (mtp)
REVERT: A  777 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.4663 (mpt90)
REVERT: A  857 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8536 (mp)
REVERT: A  861 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7870 (mt0)
REVERT: A  941 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6302 (ptpt)
REVERT: A 1041 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7168 (tppp)
REVERT: B  326 MET cc_start: 0.5380 (mpp) cc_final: 0.3744 (ttp)
REVERT: B  364 MET cc_start: 0.6691 (mpt) cc_final: 0.5819 (mpt)
REVERT: B  433 GLN cc_start: 0.5738 (OUTLIER) cc_final: 0.5483 (mt0)
REVERT: B  469 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6708 (tp30)
REVERT: B  478 GLN cc_start: 0.7500 (tp-100) cc_final: 0.6810 (tm-30)
REVERT: B  479 MET cc_start: 0.7570 (mtm) cc_final: 0.6982 (mpp)
REVERT: B  532 LYS cc_start: 0.5657 (OUTLIER) cc_final: 0.5280 (mmmm)
REVERT: B  542 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.5914 (ttm170)
REVERT: B  562 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.7163 (mtp180)
REVERT: B  575 LYS cc_start: 0.6945 (ttmt) cc_final: 0.6637 (ptmm)
  outliers start: 67
  outliers final: 33
  residues processed: 274
  average time/residue: 1.9488
  time to fit residues: 572.2305
Evaluate side-chains
  280 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 234
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 123 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9980
   chunk 120 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 119 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    4.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.184724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.146057 restraints weight = 18319.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.10
r_work: 0.3438 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3308
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3308
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.088  10793  Z= 0.233
  Angle     :  0.692  10.678  14548  Z= 0.346
  Chirality :  0.046   0.193   1570
  Planarity :  0.004   0.064   1871
  Dihedral  :  5.876  57.533   1424
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 30.84 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.71 (0.23), residues: 1270
  helix:  1.53 (0.21), residues: 598
  sheet: -0.12 (0.39), residues: 162
  loop : -0.55 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 574 
 HIS   0.007   0.001   HIS A  59 
 PHE   0.015   0.002   PHE A 980 
 TYR   0.025   0.002   TYR B 470 
 ARG   0.010   0.001   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05596 (  521)
  hydrogen bonds       : angle       4.38442 ( 1492)
  covalent geometry    : bond        0.00569 (10793)
  covalent geometry    : angle       0.69226 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 239
  time to evaluate  : 1.325 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7988 (tppt)
REVERT: A  172 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7382 (mt-10)
REVERT: A  211 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8429 (pp)
REVERT: A  263 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7712 (mm-30)
REVERT: A  697 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7834 (mpp)
REVERT: A  772 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6848 (mtp)
REVERT: A  777 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.4653 (mpt90)
REVERT: A  857 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8638 (mp)
REVERT: A  861 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7869 (mt0)
REVERT: A  941 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6376 (ptpt)
REVERT: B  364 MET cc_start: 0.6751 (mpt) cc_final: 0.5892 (mpt)
REVERT: B  433 GLN cc_start: 0.5758 (OUTLIER) cc_final: 0.5510 (mt0)
REVERT: B  469 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6679 (tp30)
REVERT: B  478 GLN cc_start: 0.7498 (tp-100) cc_final: 0.7033 (tp-100)
REVERT: B  532 LYS cc_start: 0.5704 (OUTLIER) cc_final: 0.5291 (mmmm)
REVERT: B  542 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.5863 (ttm170)
  outliers start: 64
  outliers final: 33
  residues processed: 276
  average time/residue: 1.4146
  time to fit residues: 416.2503
Evaluate side-chains
  280 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 233
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** 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 = 0.4064 r_free = 0.4064 target = 0.187222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.147362 restraints weight = 17853.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.06
r_work: 0.3445 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3311
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10793  Z= 0.140
  Angle     :  0.620  10.527  14548  Z= 0.307
  Chirality :  0.042   0.173   1570
  Planarity :  0.004   0.041   1871
  Dihedral  :  5.646  58.577   1424
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 31.61 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.93 (0.24), residues: 1270
  helix:  1.73 (0.21), residues: 599
  sheet: -0.08 (0.39), residues: 162
  loop : -0.44 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.011   0.001   PHE A 667 
 TYR   0.021   0.001   TYR A 622 
 ARG   0.010   0.000   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04684 (  521)
  hydrogen bonds       : angle       4.18556 ( 1492)
  covalent geometry    : bond        0.00331 (10793)
  covalent geometry    : angle       0.62038 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 242
  time to evaluate  : 1.229 
Fit side-chains
REVERT: A  211 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8452 (pp)
REVERT: A  278 MET cc_start: 0.7639 (mmm) cc_final: 0.7004 (mpm)
REVERT: A  281 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7413 (mtp180)
REVERT: A  297 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7675 (pp)
REVERT: A  768 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: A  772 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.6649 (mtp)
REVERT: A  777 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.4606 (mpt90)
REVERT: A  857 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8477 (mp)
REVERT: A  861 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7866 (mt0)
REVERT: A  941 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6333 (ptpt)
REVERT: A 1041 LYS cc_start: 0.7569 (tttm) cc_final: 0.7157 (tppp)
REVERT: B  364 MET cc_start: 0.6687 (mpt) cc_final: 0.5902 (mpt)
REVERT: B  433 GLN cc_start: 0.5761 (OUTLIER) cc_final: 0.5498 (mt0)
REVERT: B  469 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6711 (tp30)
REVERT: B  478 GLN cc_start: 0.7496 (tp-100) cc_final: 0.6804 (tm-30)
REVERT: B  479 MET cc_start: 0.7567 (mtm) cc_final: 0.6974 (mpp)
REVERT: B  532 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.5234 (mmmm)
REVERT: B  542 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.5933 (ttm170)
REVERT: B  562 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7206 (mtp-110)
  outliers start: 55
  outliers final: 28
  residues processed: 273
  average time/residue: 1.4140
  time to fit residues: 411.3928
Evaluate side-chains
  277 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 237
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 122 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 77 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 110 optimal weight:    0.6980
   chunk 108 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 106 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 738 GLN
A 822 ASN
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.185890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.148104 restraints weight = 17252.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.90
r_work: 0.3451 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084  10793  Z= 0.199
  Angle     :  0.683  11.061  14548  Z= 0.338
  Chirality :  0.045   0.180   1570
  Planarity :  0.004   0.061   1871
  Dihedral  :  5.605  58.253   1421
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 32.03 %
    Favored  : 63.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.80 (0.24), residues: 1270
  helix:  1.60 (0.21), residues: 598
  sheet: -0.10 (0.39), residues: 162
  loop : -0.49 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 574 
 HIS   0.006   0.001   HIS A  59 
 PHE   0.014   0.002   PHE A 980 
 TYR   0.023   0.002   TYR B 470 
 ARG   0.010   0.001   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05258 (  521)
  hydrogen bonds       : angle       4.30273 ( 1492)
  covalent geometry    : bond        0.00485 (10793)
  covalent geometry    : angle       0.68267 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 235
  time to evaluate  : 1.269 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7955 (tppt)
REVERT: A  172 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7460 (mt-10)
REVERT: A  211 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8451 (pp)
REVERT: A  281 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7398 (mtp180)
REVERT: A  622 TYR cc_start: 0.7184 (m-80) cc_final: 0.6940 (m-80)
REVERT: A  772 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.6735 (mtp)
REVERT: A  777 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.4713 (mpt90)
REVERT: A  857 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8588 (mp)
REVERT: A  861 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7866 (mt0)
REVERT: A  941 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6356 (ptpt)
REVERT: A 1041 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7250 (tppp)
REVERT: B  364 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5902 (mpt)
REVERT: B  433 GLN cc_start: 0.5760 (OUTLIER) cc_final: 0.5511 (mt0)
REVERT: B  469 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6715 (tp30)
REVERT: B  478 GLN cc_start: 0.7494 (tp-100) cc_final: 0.6845 (tm-30)
REVERT: B  532 LYS cc_start: 0.5689 (OUTLIER) cc_final: 0.5281 (mmmm)
REVERT: B  542 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.5866 (ttm170)
  outliers start: 53
  outliers final: 26
  residues processed: 264
  average time/residue: 1.5539
  time to fit residues: 437.3757
Evaluate side-chains
  273 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 232
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 125 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 119 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 75 optimal weight:    8.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.186488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.149416 restraints weight = 15843.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.70
r_work: 0.3462 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  10793  Z= 0.171
  Angle     :  0.672  11.946  14548  Z= 0.330
  Chirality :  0.044   0.171   1570
  Planarity :  0.004   0.059   1871
  Dihedral  :  5.564  58.481   1421
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 32.46 %
    Favored  : 63.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.81 (0.24), residues: 1270
  helix:  1.61 (0.21), residues: 599
  sheet: -0.12 (0.39), residues: 162
  loop : -0.48 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.012   0.002   PHE A 667 
 TYR   0.020   0.002   TYR B 470 
 ARG   0.011   0.001   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05017 (  521)
  hydrogen bonds       : angle       4.25814 ( 1492)
  covalent geometry    : bond        0.00411 (10793)
  covalent geometry    : angle       0.67216 (14548)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 236
  time to evaluate  : 2.009 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7970 (tppt)
REVERT: A  172 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7429 (mt-10)
REVERT: A  211 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8451 (pp)
REVERT: A  278 MET cc_start: 0.7677 (mmm) cc_final: 0.7025 (mpm)
REVERT: A  281 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7409 (mtp180)
REVERT: A  622 TYR cc_start: 0.7099 (m-80) cc_final: 0.6862 (m-80)
REVERT: A  768 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7559 (mm-30)
REVERT: A  772 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6692 (mtp)
REVERT: A  777 ARG cc_start: 0.6044 (OUTLIER) cc_final: 0.4586 (mpt90)
REVERT: A  857 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8559 (mp)
REVERT: A  861 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7821 (mt0)
REVERT: A 1041 LYS cc_start: 0.7574 (tttm) cc_final: 0.7182 (tppp)
REVERT: B  340 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7179 (mtm-85)
REVERT: B  364 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5923 (mpt)
REVERT: B  433 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.5481 (mt0)
REVERT: B  478 GLN cc_start: 0.7503 (tp-100) cc_final: 0.6851 (tm-30)
REVERT: B  479 MET cc_start: 0.7555 (mtm) cc_final: 0.6992 (mpp)
REVERT: B  532 LYS cc_start: 0.5661 (OUTLIER) cc_final: 0.5262 (mmmm)
REVERT: B  542 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.5916 (ttm170)
REVERT: B  562 ARG cc_start: 0.7490 (mtp180) cc_final: 0.7025 (mtp-110)
  outliers start: 47
  outliers final: 29
  residues processed: 263
  average time/residue: 1.6140
  time to fit residues: 452.7176
Evaluate side-chains
  275 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 234
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  281 ARG
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 114 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0030
   chunk 110 optimal weight:    0.2980
   chunk 72 optimal weight:    1.9990
   chunk 126 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0870
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.8772

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.189396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.149656 restraints weight = 18281.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.13
r_work: 0.3506 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10793  Z= 0.114
  Angle     :  0.622  11.567  14548  Z= 0.301
  Chirality :  0.041   0.211   1570
  Planarity :  0.003   0.044   1871
  Dihedral  :  5.287  59.193   1421
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 33.81 %
    Favored  : 63.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.24), residues: 1270
  helix:  1.81 (0.21), residues: 599
  sheet: -0.07 (0.38), residues: 166
  loop : -0.35 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.016   0.001   PHE A 937 
 TYR   0.019   0.001   TYR B 556 
 ARG   0.011   0.000   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  521)
  hydrogen bonds       : angle       4.08589 ( 1492)
  covalent geometry    : bond        0.00260 (10793)
  covalent geometry    : angle       0.62152 (14548)

===============================================================================
Job complete
usr+sys time: 13809.19 seconds
wall clock time: 242 minutes 6.04 seconds (14526.04 seconds total)