Starting phenix.real_space_refine
on Sat Jan 18 14:04:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vxy_43643/01_2025/8vxy_43643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vxy_43643/01_2025/8vxy_43643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vxy_43643/01_2025/8vxy_43643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vxy_43643/01_2025/8vxy_43643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vxy_43643/01_2025/8vxy_43643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vxy_43643/01_2025/8vxy_43643.cif"
  }
  resolution = 3.19
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     P      64      5.49       5
     S      38      5.16       5
     C    7570      2.51       5
     N    2186      2.21       5
     O    2466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12324
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 617
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "D"
      Number of atoms: 651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 651
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "A"
      Number of atoms: 1919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1919
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 7, 'TRANS': 237}
    Chain: "B"
      Number of atoms: 9106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1161, 9106
          Classifications: {'peptide': 1161}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 46, 'TRANS': 1111}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.26, per 1000 atoms: 0.59
  Number of scatterers: 12324
  At special positions: 0
  Unit cell: (116.328, 117.376, 145.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P      64     15.00
     O    2466      8.00
     N    2186      7.00
     C    7570      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: 3.43
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2612

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 6 sheets defined
      57.2% alpha, 7.3% beta
      27 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 4.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 38
    Processing helix  chain 'A' and resid 39 through 41
      No H-bonds generated for 'chain 'A' and resid 39 through 41'
    Processing helix  chain 'A' and resid 47 through 57
    Processing helix  chain 'A' and resid 60 through 70
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 5.601A  pdb=" N   GLY A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   GLU A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER A  95 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 159
      removed outlier: 3.646A  pdb=" N   VAL A 150 " --> pdb=" O   THR A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 165 through 180
    Processing helix  chain 'A' and resid 181 through 194
    Processing helix  chain 'A' and resid 198 through 200
      No H-bonds generated for 'chain 'A' and resid 198 through 200'
    Processing helix  chain 'A' and resid 213 through 224
      removed outlier: 4.438A  pdb=" N   MET A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 245
      removed outlier: 3.756A  pdb=" N   ILE A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 23 through 34
    Processing helix  chain 'B' and resid 50 through 72
    Processing helix  chain 'B' and resid 77 through 95
    Processing helix  chain 'B' and resid 103 through 118
    Processing helix  chain 'B' and resid 120 through 129
    Processing helix  chain 'B' and resid 138 through 149
    Processing helix  chain 'B' and resid 151 through 166
    Processing helix  chain 'B' and resid 169 through 182
    Processing helix  chain 'B' and resid 194 through 224
      removed outlier: 3.905A  pdb=" N   ASP B 200 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 247
      removed outlier: 4.155A  pdb=" N   LEU B 229 " --> pdb=" O   GLU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 269
      removed outlier: 4.060A  pdb=" N   HIS B 260 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 274
    Processing helix  chain 'B' and resid 285 through 299
      removed outlier: 3.949A  pdb=" N   GLU B 291 " --> pdb=" O   PRO B 287 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B 292 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 319
      removed outlier: 4.664A  pdb=" N   GLU B 313 " --> pdb=" O   PRO B 309 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   ALA B 314 " --> pdb=" O   SER B 310 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA B 315 " --> pdb=" O   GLN B 311 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY B 316 " --> pdb=" O   ARG B 312 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   VAL B 319 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 349
      removed outlier: 3.651A  pdb=" N   ALA B 339 " --> pdb=" O   LYS B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 375
      removed outlier: 3.573A  pdb=" N   THR B 373 " --> pdb=" O   THR B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 401
      removed outlier: 3.554A  pdb=" N   ALA B 397 " --> pdb=" O   MET B 393 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ARG B 399 " --> pdb=" O   GLU B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 418
      removed outlier: 3.732A  pdb=" N   ALA B 414 " --> pdb=" O   LYS B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 423
      removed outlier: 3.573A  pdb=" N   ILE B 422 " --> pdb=" O   PRO B 419 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN B 423 " --> pdb=" O   SER B 420 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 419 through 423'
    Processing helix  chain 'B' and resid 439 through 455
      removed outlier: 3.557A  pdb=" N   TYR B 445 " --> pdb=" O   ARG B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 461
    Processing helix  chain 'B' and resid 473 through 484
      removed outlier: 3.594A  pdb=" N   PHE B 479 " --> pdb=" O   GLN B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 568
      removed outlier: 3.561A  pdb=" N   ALA B 562 " --> pdb=" O   CYS B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 582
    Processing helix  chain 'B' and resid 583 through 596
      removed outlier: 3.910A  pdb=" N   GLU B 587 " --> pdb=" O   GLU B 583 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY B 596 " --> pdb=" O   LEU B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 608
    Processing helix  chain 'B' and resid 609 through 618
      removed outlier: 3.576A  pdb=" N   GLU B 618 " --> pdb=" O   SER B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 631
      removed outlier: 3.644A  pdb=" N   ALA B 628 " --> pdb=" O   SER B 624 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 655
      removed outlier: 3.796A  pdb=" N   GLU B 648 " --> pdb=" O   ALA B 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 671
      removed outlier: 4.192A  pdb=" N   LEU B 671 " --> pdb=" O   LEU B 667 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 691 through 702
    Processing helix  chain 'B' and resid 720 through 733
      removed outlier: 3.687A  pdb=" N   THR B 726 " --> pdb=" O   ASN B 722 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN B 727 " --> pdb=" O   LYS B 723 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER B 733 " --> pdb=" O   HIS B 729 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 742 through 759
      removed outlier: 3.586A  pdb=" N   LEU B 751 " --> pdb=" O   LEU B 747 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ARG B 758 " --> pdb=" O   ARG B 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 772
      removed outlier: 3.840A  pdb=" N   TYR B 769 " --> pdb=" O   ALA B 765 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 786 through 812
      removed outlier: 3.796A  pdb=" N   ARG B 790 " --> pdb=" O   SER B 786 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASP B 791 " --> pdb=" O   PRO B 787 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ILE B 792 " --> pdb=" O   GLN B 788 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER B 810 " --> pdb=" O   THR B 806 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 830
    Processing helix  chain 'B' and resid 833 through 842
      removed outlier: 3.607A  pdb=" N   ARG B 841 " --> pdb=" O   ARG B 837 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 844 through 866
      removed outlier: 3.582A  pdb=" N   ARG B 848 " --> pdb=" O   ASP B 844 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU B 850 " --> pdb=" O   ASN B 846 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 867 through 878
    Processing helix  chain 'B' and resid 880 through 890
      removed outlier: 3.854A  pdb=" N   ILE B 890 " --> pdb=" O   ARG B 886 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 903
    Processing helix  chain 'B' and resid 909 through 925
    Processing helix  chain 'B' and resid 927 through 931
      removed outlier: 3.607A  pdb=" N   ILE B 931 " --> pdb=" O   TYR B 928 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 937 through 942
      removed outlier: 3.969A  pdb=" N   GLY B 941 " --> pdb=" O   GLY B 937 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 948
      removed outlier: 3.732A  pdb=" N   TRP B 946 " --> pdb=" O   ILE B 942 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B 947 " --> pdb=" O   LEU B 943 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 961 through 966
    Processing helix  chain 'B' and resid 966 through 971
    Processing helix  chain 'B' and resid 974 through 990
      removed outlier: 3.686A  pdb=" N   THR B 987 " --> pdb=" O   ARG B 983 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1003 through 1006
      removed outlier: 4.073A  pdb=" N   GLY B1006 " --> pdb=" O   TYR B1003 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1003 through 1006'
    Processing helix  chain 'B' and resid 1007 through 1013
      removed outlier: 3.912A  pdb=" N   VAL B1012 " --> pdb=" O   ALA B1008 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLU B1013 " --> pdb=" O   VAL B1009 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1021 through 1028
      removed outlier: 3.509A  pdb=" N   ILE B1025 " --> pdb=" O   SER B1021 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY B1028 " --> pdb=" O   LEU B1024 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1033 through 1040
      removed outlier: 4.281A  pdb=" N   THR B1040 " --> pdb=" O   ILE B1036 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1050 through 1056
      removed outlier: 3.845A  pdb=" N   ARG B1054 " --> pdb=" O   GLN B1050 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1059 through 1067
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11
      removed outlier: 3.676A  pdb=" N   ASP A   9 " --> pdb=" O   THR A  24 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR A  24 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   GLN A  21 " --> pdb=" O   CYS A 235 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ARG A 237 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   ILE A  23 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ARG A 203 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   PHE A 134 " --> pdb=" O   ARG A 203 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU A 205 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LYS A 136 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   PHE A 207 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   ALA A 138 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LEU A 209 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 381 through 383
      removed outlier: 3.776A  pdb=" N   SER B 382 " --> pdb=" O   ILE B 403 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL B 405 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL B 326 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 524 through 531
      removed outlier: 8.639A  pdb=" N   VAL B 526 " --> pdb=" O   LEU B 517 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   LEU B 517 " --> pdb=" O   VAL B 526 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   ARG B 528 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   LEU B 515 " --> pdb=" O   ARG B 528 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   GLY B 504 " --> pdb=" O   TYR B 715 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ILE B 717 " --> pdb=" O   GLY B 504 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   VAL B 506 " --> pdb=" O   ILE B 717 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 572 through 573
      removed outlier: 6.870A  pdb=" N   VAL B 572 " --> pdb=" O   THR B 661 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1095 through 1096
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1099 through 1102
      removed outlier: 3.770A  pdb=" N   GLU B1153 " --> pdb=" O   MET B1162 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL B1152 " --> pdb=" O   LEU B1116 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   HIS B1125 " --> pdb=" O   SER B1137 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   SER B1137 " --> pdb=" O   HIS B1125 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   VAL B1127 " --> pdb=" O   LEU B1135 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1578 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      54 hydrogen bonds
      108 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 6.10

  Time building geometry restraints manager: 3.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3222
        1.33 -     1.45: 2517
        1.45 -     1.57: 6762
        1.57 -     1.69: 126
        1.69 -     1.81: 64
  Bond restraints: 12691
  Sorted by residual:
  bond pdb=" C4  ATP B1201 "
       pdb=" C5  ATP B1201 "
    ideal  model  delta    sigma   weight residual
    1.388  1.463 -0.075 1.00e-02 1.00e+04 5.66e+01
  bond pdb=" C5  ATP B1201 "
       pdb=" C6  ATP B1201 "
    ideal  model  delta    sigma   weight residual
    1.409  1.473 -0.064 1.00e-02 1.00e+04 4.07e+01
  bond pdb=" C4  ATP B1201 "
       pdb=" N9  ATP B1201 "
    ideal  model  delta    sigma   weight residual
    1.374  1.325  0.049 1.00e-02 1.00e+04 2.44e+01
  bond pdb=" C5  ATP B1201 "
       pdb=" N7  ATP B1201 "
    ideal  model  delta    sigma   weight residual
    1.387  1.340  0.047 1.00e-02 1.00e+04 2.22e+01
  bond pdb=" C8  ATP B1201 "
       pdb=" N7  ATP B1201 "
    ideal  model  delta    sigma   weight residual
    1.310  1.353 -0.043 1.00e-02 1.00e+04 1.87e+01
  ... (remaining 12686 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.71: 17391
        3.71 -     7.43: 39
        7.43 -    11.14: 58
       11.14 -    14.85: 1
       14.85 -    18.56: 2
  Bond angle restraints: 17491
  Sorted by residual:
  angle pdb=" PA  ATP B1201 "
        pdb=" O3A ATP B1201 "
        pdb=" PB  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     136.83  118.27   18.56 1.00e+00 1.00e+00 3.45e+02
  angle pdb=" PB  ATP B1201 "
        pdb=" O3B ATP B1201 "
        pdb=" PG  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     139.87  122.96   16.91 1.00e+00 1.00e+00 2.86e+02
  angle pdb=" C5  ATP B1201 "
        pdb=" C4  ATP B1201 "
        pdb=" N3  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     126.80  119.42    7.38 1.00e+00 1.00e+00 5.45e+01
  angle pdb=" N3  ATP B1201 "
        pdb=" C4  ATP B1201 "
        pdb=" N9  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     127.04  134.58   -7.54 1.15e+00 7.59e-01 4.31e+01
  angle pdb=" N1  ATP B1201 "
        pdb=" C2  ATP B1201 "
        pdb=" N3  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     128.69  123.49    5.20 1.00e+00 1.00e+00 2.70e+01
  ... (remaining 17486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 6676
       17.73 -    35.45: 551
       35.45 -    53.18: 243
       53.18 -    70.90: 62
       70.90 -    88.63: 6
  Dihedral angle restraints: 7538
    sinusoidal: 3493
      harmonic: 4045
  Sorted by residual:
  dihedral pdb=" CA  HIS B 638 "
           pdb=" C   HIS B 638 "
           pdb=" N   GLY B 639 "
           pdb=" CA  GLY B 639 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.25   18.75     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  PHE B 966 "
           pdb=" C   PHE B 966 "
           pdb=" N   VAL B 967 "
           pdb=" CA  VAL B 967 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.38  -16.62     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ILE B  94 "
           pdb=" C   ILE B  94 "
           pdb=" N   ALA B  95 "
           pdb=" CA  ALA B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.89  -16.11     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 7535 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1853
       0.090 -    0.180: 86
       0.180 -    0.270: 0
       0.270 -    0.360: 3
       0.360 -    0.450: 28
  Chirality restraints: 1970
  Sorted by residual:
  chirality pdb=" P    DA D  11 "
            pdb=" OP1  DA D  11 "
            pdb=" OP2  DA D  11 "
            pdb=" O5'  DA D  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.80   -0.45 2.00e-01 2.50e+01 5.05e+00
  chirality pdb=" P    DA D  21 "
            pdb=" OP1  DA D  21 "
            pdb=" OP2  DA D  21 "
            pdb=" O5'  DA D  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.77   -0.43 2.00e-01 2.50e+01 4.56e+00
  chirality pdb=" P    DA D  20 "
            pdb=" OP1  DA D  20 "
            pdb=" OP2  DA D  20 "
            pdb=" O5'  DA D  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.76   -0.41 2.00e-01 2.50e+01 4.22e+00
  ... (remaining 1967 not shown)

  Planarity restraints: 2057
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  12 "   -0.029 2.00e-02 2.50e+03   1.30e-02 4.20e+00
        pdb=" N1   DT C  12 "    0.024 2.00e-02 2.50e+03
        pdb=" C2   DT C  12 "    0.004 2.00e-02 2.50e+03
        pdb=" O2   DT C  12 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DT C  12 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DT C  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" O4   DT C  12 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5   DT C  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C7   DT C  12 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DT C  12 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 817 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 818 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 818 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 818 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  28 "   -0.007 2.00e-02 2.50e+03   1.47e-02 2.17e+00
        pdb=" C   ALA A  28 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ALA A  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLU A  29 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2054 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1587
        2.75 -     3.29: 12809
        3.29 -     3.83: 22503
        3.83 -     4.36: 26272
        4.36 -     4.90: 42139
  Nonbonded interactions: 105310
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 314 "
            pdb=" OG  SER B 318 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   GLU B 367 "
            pdb=" OG  SER B 371 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ARG B 317 "
            pdb=" NH2 ARG B 462 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OG1 THR B 357 "
            pdb=" OG  SER B 363 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   ASN B 773 "
            pdb=" OH  TYR B 861 "
     model   vdw
     2.239 3.040
  ... (remaining 105305 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=1.00 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     34.370
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6095
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   0.075  12691  Z= 0.176
  Angle     :  0.807  18.565  17491  Z= 0.416
  Chirality :  0.062   0.450   1970
  Planarity :  0.003   0.040   2057
  Dihedral  : 16.144  88.626   4926
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.15 (0.23), residues: 1400
  helix:  1.01 (0.21), residues: 674
  sheet: -0.88 (0.50), residues: 119
  loop : -1.19 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  35 
 HIS   0.003   0.001   HIS B 260 
 PHE   0.019   0.001   PHE B 256 
 TYR   0.013   0.001   TYR B  58 
 ARG   0.003   0.000   ARG B 841 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2473 (tpp) cc_final: 0.0976 (ptt)
REVERT: A   14 ASN cc_start: 0.7933 (p0) cc_final: 0.7339 (t0)
REVERT: A   19 TYR cc_start: 0.5912 (t80) cc_final: 0.5592 (t80)
REVERT: A   86 PHE cc_start: 0.5694 (m-80) cc_final: 0.5412 (m-80)
REVERT: A  123 ILE cc_start: 0.6147 (tt) cc_final: 0.5628 (tp)
REVERT: A  152 GLU cc_start: 0.7561 (pt0) cc_final: 0.7232 (pp20)
REVERT: A  215 GLU cc_start: 0.7001 (tt0) cc_final: 0.6721 (tp30)
REVERT: B   23 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6442 (mtp85)
REVERT: B  525 TRP cc_start: 0.7287 (p90) cc_final: 0.6675 (p90)
REVERT: B  624 SER cc_start: 0.8462 (t) cc_final: 0.8002 (p)
REVERT: B  650 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6196 (tt0)
REVERT: B 1083 LEU cc_start: 0.5640 (tp) cc_final: 0.5178 (tp)
REVERT: B 1141 ARG cc_start: 0.7288 (mtp-110) cc_final: 0.7030 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.3247
  time to fit residues: 114.0392
Evaluate side-chains
  153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0010
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 114 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    1.0790

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
A 130 GLN
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 ASN
B 502 GLN
** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 HIS
B 959 GLN
B 989 ASN
B1026 GLN
B1068 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.225901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.188721 restraints weight = 18233.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4523 rms_B_bonded: 2.29
r_work: 0.4357 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6395
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  12691  Z= 0.258
  Angle     :  0.664  10.382  17491  Z= 0.352
  Chirality :  0.043   0.198   1970
  Planarity :  0.005   0.039   2057
  Dihedral  : 19.213  88.630   2319
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  8.48 %
    Favored  : 90.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.49 (0.22), residues: 1400
  helix:  0.62 (0.19), residues: 726
  sheet: -1.02 (0.43), residues: 147
  loop : -1.40 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 797 
 HIS   0.020   0.002   HIS B1068 
 PHE   0.028   0.002   PHE B 199 
 TYR   0.018   0.002   TYR B  58 
 ARG   0.007   0.001   ARG B 514 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 194
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2181 (tpp) cc_final: 0.0531 (ptt)
REVERT: A   14 ASN cc_start: 0.7940 (p0) cc_final: 0.7668 (t0)
REVERT: A  217 MET cc_start: 0.7228 (ptp) cc_final: 0.7000 (ptt)
REVERT: B   23 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7042 (mtp85)
REVERT: B  144 LEU cc_start: 0.6825 (tp) cc_final: 0.6524 (tp)
REVERT: B  680 MET cc_start: 0.7473 (mmm) cc_final: 0.7093 (mmt)
REVERT: B  900 ASP cc_start: 0.6496 (t70) cc_final: 0.6015 (t0)
REVERT: B 1083 LEU cc_start: 0.6006 (tp) cc_final: 0.5356 (tp)
REVERT: B 1102 MET cc_start: 0.6789 (mmt) cc_final: 0.6468 (mmm)
  outliers start: 11
  outliers final: 4
  residues processed: 200
  average time/residue: 0.3001
  time to fit residues: 82.1318
Evaluate side-chains
  148 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  623 HIS
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue 1012 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0470
   chunk 119 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 68 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 231 GLN
A 241 HIS
B 245 GLN
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 772 ASN
** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1064 HIS ** 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 = 0.4908 r_free = 0.4908 target = 0.226999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.189517 restraints weight = 18563.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4533 rms_B_bonded: 2.27
r_work: 0.4380 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.4380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6371
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12691  Z= 0.195
  Angle     :  0.599   9.260  17491  Z= 0.321
  Chirality :  0.041   0.190   1970
  Planarity :  0.004   0.042   2057
  Dihedral  : 19.150  88.265   2319
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 11.99 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.23), residues: 1400
  helix:  0.67 (0.20), residues: 726
  sheet: -1.37 (0.41), residues: 156
  loop : -1.38 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B1105 
 HIS   0.004   0.001   HIS B1064 
 PHE   0.032   0.002   PHE A  86 
 TYR   0.015   0.001   TYR B 445 
 ARG   0.008   0.000   ARG B1160 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2233 (tpp) cc_final: 0.0593 (ptt)
REVERT: A   14 ASN cc_start: 0.7961 (p0) cc_final: 0.7734 (t0)
REVERT: B   23 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7144 (mtp180)
REVERT: B  680 MET cc_start: 0.7337 (mmm) cc_final: 0.6963 (mmt)
REVERT: B  712 LEU cc_start: 0.7656 (tp) cc_final: 0.7344 (mt)
REVERT: B  755 MET cc_start: 0.4838 (ptm) cc_final: 0.4496 (ptp)
REVERT: B  979 MET cc_start: 0.5815 (ptp) cc_final: 0.5615 (ptp)
REVERT: B 1070 TRP cc_start: 0.5548 (t60) cc_final: 0.5266 (t60)
REVERT: B 1083 LEU cc_start: 0.6100 (tp) cc_final: 0.5536 (mp)
REVERT: B 1102 MET cc_start: 0.6769 (mmt) cc_final: 0.6373 (mmm)
  outliers start: 12
  outliers final: 5
  residues processed: 180
  average time/residue: 0.2777
  time to fit residues: 69.9432
Evaluate side-chains
  149 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 144
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue 1137 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 136 optimal weight:    3.9990
   chunk 131 optimal weight:    0.3980
   chunk 83 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.219729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.181571 restraints weight = 18299.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.4452 rms_B_bonded: 2.23
r_work: 0.4297 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6608
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  12691  Z= 0.341
  Angle     :  0.704  10.232  17491  Z= 0.369
  Chirality :  0.045   0.259   1970
  Planarity :  0.005   0.049   2057
  Dihedral  : 19.238  91.305   2319
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.36 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -1.02 (0.22), residues: 1400
  helix:  0.26 (0.19), residues: 730
  sheet: -1.66 (0.40), residues: 147
  loop : -1.63 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B1105 
 HIS   0.006   0.002   HIS B1064 
 PHE   0.020   0.002   PHE B 270 
 TYR   0.022   0.002   TYR B  58 
 ARG   0.008   0.001   ARG B 595 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2521 (tpp) cc_final: 0.0715 (ptt)
REVERT: A   14 ASN cc_start: 0.7986 (p0) cc_final: 0.7752 (t0)
REVERT: A   78 ARG cc_start: 0.5774 (mmt-90) cc_final: 0.4835 (mmt180)
REVERT: A  220 THR cc_start: 0.8260 (p) cc_final: 0.8056 (t)
REVERT: B  102 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7417 (ttm-80)
REVERT: B  140 ILE cc_start: 0.7376 (mt) cc_final: 0.7076 (mt)
REVERT: B  234 GLU cc_start: 0.6729 (pp20) cc_final: 0.6319 (pp20)
REVERT: B  383 MET cc_start: 0.7934 (ptm) cc_final: 0.7498 (ptm)
REVERT: B  417 ASN cc_start: 0.6511 (m-40) cc_final: 0.6228 (m-40)
REVERT: B  555 LYS cc_start: 0.6514 (mtpp) cc_final: 0.6306 (mtpp)
REVERT: B  597 LEU cc_start: 0.5021 (OUTLIER) cc_final: 0.4590 (pp)
REVERT: B 1078 MET cc_start: 0.6187 (mmt) cc_final: 0.5856 (mmt)
REVERT: B 1102 MET cc_start: 0.7049 (mmt) cc_final: 0.6555 (mmm)
REVERT: B 1162 MET cc_start: 0.8086 (tmm) cc_final: 0.7834 (tmm)
  outliers start: 28
  outliers final: 16
  residues processed: 192
  average time/residue: 0.3097
  time to fit residues: 82.0617
Evaluate side-chains
  153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  623 HIS
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  881 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue  885 LEU
Chi-restraints excluded: chain B residue 1104 ASP
Chi-restraints excluded: chain B residue 1108 THR
Chi-restraints excluded: chain B residue 1121 VAL
Chi-restraints excluded: chain B residue 1137 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 110 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 672 ASN
B1026 GLN
** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1097 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.223524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.185968 restraints weight = 18365.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.4502 rms_B_bonded: 2.29
r_work: 0.4363 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12691  Z= 0.222
  Angle     :  0.625   9.017  17491  Z= 0.332
  Chirality :  0.042   0.241   1970
  Planarity :  0.004   0.045   2057
  Dihedral  : 19.123  88.568   2319
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.81 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.87 (0.22), residues: 1400
  helix:  0.42 (0.19), residues: 732
  sheet: -1.91 (0.38), residues: 156
  loop : -1.50 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B1105 
 HIS   0.004   0.001   HIS B 260 
 PHE   0.016   0.002   PHE B 718 
 TYR   0.016   0.001   TYR B  58 
 ARG   0.009   0.001   ARG B 500 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 1.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2629 (tpp) cc_final: 0.0850 (ptt)
REVERT: A   78 ARG cc_start: 0.5697 (mmt-90) cc_final: 0.4938 (mmt180)
REVERT: A  230 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.5856 (t0)
REVERT: B  140 ILE cc_start: 0.7270 (mt) cc_final: 0.6873 (mp)
REVERT: B  234 GLU cc_start: 0.6582 (pp20) cc_final: 0.6351 (pp20)
REVERT: B  383 MET cc_start: 0.7824 (ptm) cc_final: 0.7512 (ptm)
REVERT: B  417 ASN cc_start: 0.6026 (m-40) cc_final: 0.5762 (m110)
REVERT: B  680 MET cc_start: 0.7433 (mmm) cc_final: 0.6819 (mmt)
REVERT: B 1021 SER cc_start: 0.6225 (OUTLIER) cc_final: 0.5802 (m)
REVERT: B 1078 MET cc_start: 0.6108 (mmt) cc_final: 0.5816 (mmt)
REVERT: B 1083 LEU cc_start: 0.6419 (tp) cc_final: 0.5854 (mt)
REVERT: B 1102 MET cc_start: 0.6991 (mmt) cc_final: 0.6465 (mmm)
  outliers start: 25
  outliers final: 13
  residues processed: 175
  average time/residue: 0.3116
  time to fit residues: 75.2213
Evaluate side-chains
  149 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  623 HIS
Chi-restraints excluded: chain B residue  672 ASN
Chi-restraints excluded: chain B residue  712 LEU
Chi-restraints excluded: chain B residue 1021 SER
Chi-restraints excluded: chain B residue 1104 ASP
Chi-restraints excluded: chain B residue 1108 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 104 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   chunk 111 optimal weight:    0.9980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1026 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.223845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.186521 restraints weight = 18629.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.4509 rms_B_bonded: 2.24
r_work: 0.4357 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12691  Z= 0.213
  Angle     :  0.628  10.607  17491  Z= 0.328
  Chirality :  0.042   0.252   1970
  Planarity :  0.004   0.044   2057
  Dihedral  : 19.053  87.031   2319
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.84 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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 (0.22), residues: 1400
  helix:  0.49 (0.19), residues: 735
  sheet: -1.88 (0.38), residues: 156
  loop : -1.48 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B1105 
 HIS   0.004   0.001   HIS B 260 
 PHE   0.015   0.001   PHE B 718 
 TYR   0.016   0.001   TYR B  58 
 ARG   0.008   0.000   ARG B 500 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2434 (tpp) cc_final: 0.0768 (ptt)
REVERT: A   78 ARG cc_start: 0.5819 (mmt-90) cc_final: 0.5042 (mmt180)
REVERT: A  217 MET cc_start: 0.6969 (ptt) cc_final: 0.6757 (ptt)
REVERT: A  231 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.5869 (mp-120)
REVERT: B  140 ILE cc_start: 0.7380 (mt) cc_final: 0.6977 (mp)
REVERT: B  383 MET cc_start: 0.7805 (ptm) cc_final: 0.7476 (ptm)
REVERT: B  417 ASN cc_start: 0.5879 (m-40) cc_final: 0.5636 (m110)
REVERT: B  555 LYS cc_start: 0.6694 (mtpp) cc_final: 0.6413 (mtpp)
REVERT: B  680 MET cc_start: 0.7342 (mmm) cc_final: 0.6751 (mmt)
REVERT: B 1021 SER cc_start: 0.6112 (OUTLIER) cc_final: 0.5694 (m)
REVERT: B 1102 MET cc_start: 0.7041 (mmt) cc_final: 0.6469 (mmm)
  outliers start: 24
  outliers final: 14
  residues processed: 160
  average time/residue: 0.2768
  time to fit residues: 62.7113
Evaluate side-chains
  147 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  231 GLN
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  211 MET
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  623 HIS
Chi-restraints excluded: chain B residue  712 LEU
Chi-restraints excluded: chain B residue 1021 SER
Chi-restraints excluded: chain B residue 1104 ASP
Chi-restraints excluded: chain B residue 1108 THR
Chi-restraints excluded: chain B residue 1137 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 99 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 144 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 143 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS
A 156 ASN
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1064 HIS ** 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 = 0.4837 r_free = 0.4837 target = 0.218934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.179772 restraints weight = 18415.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4437 rms_B_bonded: 2.29
r_work: 0.4283 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12691  Z= 0.354
  Angle     :  0.720  10.594  17491  Z= 0.375
  Chirality :  0.046   0.270   1970
  Planarity :  0.005   0.052   2057
  Dihedral  : 19.101  89.364   2319
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.95 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -1.13 (0.22), residues: 1400
  helix:  0.25 (0.19), residues: 720
  sheet: -1.99 (0.39), residues: 143
  loop : -1.68 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP B1105 
 HIS   0.009   0.002   HIS A 167 
 PHE   0.018   0.002   PHE B 718 
 TYR   0.025   0.002   TYR B 445 
 ARG   0.007   0.001   ARG B 500 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2647 (tpp) cc_final: 0.0761 (ptt)
REVERT: A   78 ARG cc_start: 0.5859 (mmt-90) cc_final: 0.5015 (mpt180)
REVERT: A  230 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7327 (m-40)
REVERT: A  231 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.5903 (mp-120)
REVERT: B  144 LEU cc_start: 0.7026 (tp) cc_final: 0.6808 (tp)
REVERT: B  211 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4164 (mmt)
REVERT: B  383 MET cc_start: 0.7834 (ptm) cc_final: 0.7522 (ptm)
REVERT: B  613 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7784 (mt)
REVERT: B  680 MET cc_start: 0.7501 (mmm) cc_final: 0.6893 (mmp)
REVERT: B 1083 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6697 (mt)
REVERT: B 1102 MET cc_start: 0.6882 (mmt) cc_final: 0.6305 (mmm)
  outliers start: 26
  outliers final: 15
  residues processed: 161
  average time/residue: 0.2994
  time to fit residues: 66.8021
Evaluate side-chains
  149 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 HIS
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  231 GLN
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  211 MET
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  623 HIS
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  712 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue  946 TRP
Chi-restraints excluded: chain B residue 1021 SER
Chi-restraints excluded: chain B residue 1083 LEU
Chi-restraints excluded: chain B residue 1137 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 126 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS
A 156 ASN
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1026 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.222898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.185624 restraints weight = 18591.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.4499 rms_B_bonded: 2.22
r_work: 0.4348 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
moved from start:          0.4902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12691  Z= 0.211
  Angle     :  0.641  10.250  17491  Z= 0.336
  Chirality :  0.043   0.243   1970
  Planarity :  0.005   0.046   2057
  Dihedral  : 18.974  85.817   2319
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.55 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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 (0.22), residues: 1400
  helix:  0.41 (0.19), residues: 725
  sheet: -2.15 (0.37), residues: 154
  loop : -1.55 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B1105 
 HIS   0.015   0.001   HIS A  18 
 PHE   0.012   0.002   PHE B 718 
 TYR   0.015   0.001   TYR B  58 
 ARG   0.009   0.001   ARG B 163 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2538 (tpp) cc_final: 0.0773 (ptt)
REVERT: A   31 MET cc_start: 0.5395 (mtt) cc_final: 0.5184 (ptp)
REVERT: A   78 ARG cc_start: 0.5825 (mmt-90) cc_final: 0.4982 (mpt180)
REVERT: A  230 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6006 (t0)
REVERT: A  231 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6168 (mp-120)
REVERT: B  234 GLU cc_start: 0.6497 (pp20) cc_final: 0.6122 (pp20)
REVERT: B  383 MET cc_start: 0.7836 (ptm) cc_final: 0.7547 (ptm)
REVERT: B  680 MET cc_start: 0.7294 (mmm) cc_final: 0.6755 (mmt)
REVERT: B  914 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6732 (mt)
REVERT: B 1021 SER cc_start: 0.6268 (OUTLIER) cc_final: 0.5873 (m)
REVERT: B 1083 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6782 (mt)
REVERT: B 1102 MET cc_start: 0.6792 (mmt) cc_final: 0.6223 (mmm)
  outliers start: 19
  outliers final: 9
  residues processed: 165
  average time/residue: 0.3003
  time to fit residues: 69.4888
Evaluate side-chains
  153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 HIS
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  231 GLN
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  617 GLU
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue 1021 SER
Chi-restraints excluded: chain B residue 1083 LEU
Chi-restraints excluded: chain B residue 1137 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 139 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 130 optimal weight:    0.4980
   chunk 56 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    0.1980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS
A 156 ASN
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 756 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.225072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.187284 restraints weight = 18256.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.4524 rms_B_bonded: 2.22
r_work: 0.4355 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  12691  Z= 0.300
  Angle     :  0.683   9.606  17491  Z= 0.357
  Chirality :  0.045   0.264   1970
  Planarity :  0.005   0.050   2057
  Dihedral  : 18.970  86.360   2319
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 18.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 18.15 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -1.08 (0.22), residues: 1400
  helix:  0.33 (0.19), residues: 720
  sheet: -2.23 (0.37), residues: 157
  loop : -1.61 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B1105 
 HIS   0.012   0.002   HIS A  18 
 PHE   0.015   0.002   PHE B 718 
 TYR   0.021   0.002   TYR B  58 
 ARG   0.007   0.001   ARG B 500 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2735 (tpp) cc_final: 0.0780 (ptt)
REVERT: A   78 ARG cc_start: 0.5826 (mmt-90) cc_final: 0.4990 (mpt180)
REVERT: A  230 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.7270 (m-40)
REVERT: A  231 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.5949 (mp-120)
REVERT: B  234 GLU cc_start: 0.6476 (pp20) cc_final: 0.6120 (pp20)
REVERT: B  383 MET cc_start: 0.7835 (ptm) cc_final: 0.7549 (ptm)
REVERT: B  555 LYS cc_start: 0.6815 (mtpp) cc_final: 0.6589 (mtpp)
REVERT: B  680 MET cc_start: 0.7307 (mmm) cc_final: 0.6731 (mmp)
REVERT: B 1083 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6820 (mt)
REVERT: B 1102 MET cc_start: 0.6832 (mmt) cc_final: 0.6275 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 156
  average time/residue: 0.3006
  time to fit residues: 65.6683
Evaluate side-chains
  153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 HIS
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  231 GLN
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  623 HIS
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  946 TRP
Chi-restraints excluded: chain B residue 1021 SER
Chi-restraints excluded: chain B residue 1083 LEU
Chi-restraints excluded: chain B residue 1137 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 110 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 112 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 140 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS
A 156 ASN
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 756 HIS
B1026 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.227897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.191458 restraints weight = 18062.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.4563 rms_B_bonded: 2.14
r_work: 0.4416 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.5124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12691  Z= 0.215
  Angle     :  0.644   9.844  17491  Z= 0.338
  Chirality :  0.043   0.236   1970
  Planarity :  0.005   0.045   2057
  Dihedral  : 18.892  85.175   2319
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.49 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.94 (0.22), residues: 1400
  helix:  0.45 (0.19), residues: 723
  sheet: -2.22 (0.37), residues: 157
  loop : -1.55 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B1105 
 HIS   0.010   0.001   HIS B 756 
 PHE   0.012   0.002   PHE B 718 
 TYR   0.015   0.001   TYR B  58 
 ARG   0.008   0.001   ARG B 484 

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2688 (tpp) cc_final: 0.0605 (ptp)
REVERT: A   78 ARG cc_start: 0.5840 (mmt-90) cc_final: 0.5003 (mpt180)
REVERT: A  230 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6040 (t0)
REVERT: A  231 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6259 (mp-120)
REVERT: B  102 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7372 (mpt180)
REVERT: B  172 LYS cc_start: 0.7527 (tptt) cc_final: 0.7198 (tptp)
REVERT: B  234 GLU cc_start: 0.6401 (pp20) cc_final: 0.6019 (pp20)
REVERT: B  383 MET cc_start: 0.7805 (ptm) cc_final: 0.7545 (ptm)
REVERT: B  555 LYS cc_start: 0.6828 (mtpp) cc_final: 0.6586 (mtpp)
REVERT: B  680 MET cc_start: 0.7215 (mmm) cc_final: 0.6704 (mmt)
REVERT: B 1021 SER cc_start: 0.6292 (OUTLIER) cc_final: 0.5877 (m)
REVERT: B 1083 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6858 (mt)
REVERT: B 1102 MET cc_start: 0.6744 (mmt) cc_final: 0.6199 (mmm)
  outliers start: 15
  outliers final: 10
  residues processed: 157
  average time/residue: 0.3088
  time to fit residues: 67.4922
Evaluate side-chains
  154 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 HIS
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  231 GLN
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  946 TRP
Chi-restraints excluded: chain B residue 1021 SER
Chi-restraints excluded: chain B residue 1083 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 133 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 125 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.227589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.190475 restraints weight = 18088.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 2.24
r_work: 0.4393 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.5189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12691  Z= 0.231
  Angle     :  0.649   9.580  17491  Z= 0.340
  Chirality :  0.044   0.520   1970
  Planarity :  0.005   0.045   2057
  Dihedral  : 18.848  85.006   2319
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.98 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.92 (0.22), residues: 1400
  helix:  0.46 (0.19), residues: 724
  sheet: -2.18 (0.37), residues: 159
  loop : -1.53 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B1105 
 HIS   0.005   0.001   HIS A  18 
 PHE   0.012   0.001   PHE B 718 
 TYR   0.016   0.002   TYR B  58 
 ARG   0.007   0.001   ARG B 163 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5979.49 seconds
wall clock time: 106 minutes 57.42 seconds (6417.42 seconds total)