Starting phenix.real_space_refine
on Sat Jan 18 15:31:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z1f_39726/01_2025/8z1f_39726.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z1f_39726/01_2025/8z1f_39726.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z1f_39726/01_2025/8z1f_39726.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z1f_39726/01_2025/8z1f_39726.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z1f_39726/01_2025/8z1f_39726.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z1f_39726/01_2025/8z1f_39726.cif"
  }
  resolution = 4.3
  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=   0.000 sd=   0.004
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      67      5.49       5
     S      38      5.16       5
     C    3948      2.51       5
     N    1161      2.21       5
     O    1419      1.98       5
     H    5934      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12569
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "T"
      Number of atoms: 2122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 2122
          Classifications: {'RNA': 66}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 15, 'rna3p': 50}
    Chain: "A"
      Number of atoms: 10440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 668, 10440
          Classifications: {'peptide': 668}
          Link IDs: {'PTRANS': 40, 'TRANS': 627}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 7
          Unusual residues: {' ZN': 2, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 8.26, per 1000 atoms: 0.66
  Number of scatterers: 12569
  At special positions: 0
  Unit cell: (70.484, 89.946, 128.87, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      38     16.00
     P      67     15.00
     O    1419      8.00
     N    1161      7.00
     C    3948      6.00
     H    5934      1.00
    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: 3.22
  Conformation dependent library (CDL) restraints added in 925.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" ND1 HIS A 548 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 546 "
        pdb="ZN    ZN A 901 " - pdb="ZN    ZN A 902 "
      pdb="  ZN A 902 "
        pdb="ZN    ZN A 902 " - pdb=" NE2 HIS A 724 "


  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1254

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      37.9% alpha, 11.4% beta
      12 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 5.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 98
      removed outlier: 4.731A  pdb=" N   GLN A  96 " --> pdb=" O   GLN A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 119
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 141 through 143
      No H-bonds generated for 'chain 'A' and resid 141 through 143'
    Processing helix  chain 'A' and resid 144 through 156
      removed outlier: 3.685A  pdb=" N   LEU A 148 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   LYS A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   ILE A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   PHE A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.889A  pdb=" N   ILE A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY A 281 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 3.562A  pdb=" N   LEU A 296 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 321
      removed outlier: 3.532A  pdb=" N   ILE A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
      removed outlier: 3.557A  pdb=" N   ARG A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 351
      removed outlier: 3.676A  pdb=" N   ASP A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 361
      removed outlier: 3.924A  pdb=" N   PHE A 361 " --> pdb=" O   TRP A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 393
    Processing helix  chain 'A' and resid 442 through 451
      removed outlier: 4.007A  pdb=" N   VAL A 448 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 449 " --> pdb=" O   GLU A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 468
    Processing helix  chain 'A' and resid 519 through 525
    Processing helix  chain 'A' and resid 528 through 530
      No H-bonds generated for 'chain 'A' and resid 528 through 530'
    Processing helix  chain 'A' and resid 531 through 539
      removed outlier: 3.617A  pdb=" N   GLY A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 552
    Processing helix  chain 'A' and resid 554 through 569
      removed outlier: 3.571A  pdb=" N   GLN A 561 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 567 " --> pdb=" O   GLU A 563 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LEU A 569 " --> pdb=" O   ALA A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 595
      removed outlier: 4.116A  pdb=" N   TRP A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 602
    Processing helix  chain 'A' and resid 607 through 611
    Processing helix  chain 'A' and resid 620 through 632
    Processing helix  chain 'A' and resid 670 through 678
      removed outlier: 3.579A  pdb=" N   VAL A 674 " --> pdb=" O   CYS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 701
      removed outlier: 3.530A  pdb=" N   LYS A 700 " --> pdb=" O   GLU A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 716
      removed outlier: 3.934A  pdb=" N   ASN A 716 " --> pdb=" O   GLY A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 762
    Processing helix  chain 'A' and resid 763 through 772
      removed outlier: 3.627A  pdb=" N   PHE A 771 " --> pdb=" O   LEU A 767 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 164
      removed outlier: 6.582A  pdb=" N   ARG A  82 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   PHE A 109 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   LEU A  84 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU A 432 " --> pdb=" O   GLN A 426 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174
      removed outlier: 3.593A  pdb=" N   TYR A 173 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   PHE A 243 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL A 308 " --> pdb=" O   PHE A 243 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   CYS A 245 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   PHE A 306 " --> pdb=" O   CYS A 245 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ALA A 305 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   VAL A 340 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL A 307 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   HIS A 342 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL A 309 " --> pdb=" O   HIS A 342 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286
    Processing sheet with id=AA4, first strand: chain 'A' and resid 482 through 484
    Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 543
    Processing sheet with id=AA6, first strand: chain 'A' and resid 634 through 638
      removed outlier: 3.773A  pdb=" N   GLU A 636 " --> pdb=" O   VAL A 654 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 654 " --> pdb=" O   GLU A 636 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   CYS A 651 " --> pdb=" O   TYR A 663 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   GLU A 686 " --> pdb=" O   SER A 664 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU A 683 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   LEU A 722 " --> pdb=" O   LEU A 683 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   HIS A 685 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   HIS A 724 " --> pdb=" O   HIS A 685 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ILE A 720 " --> pdb=" O   GLY A 744 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    438 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 5.22

  Time building geometry restraints manager: 3.91 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5914
        1.03 -     1.23: 39
        1.23 -     1.42: 3016
        1.42 -     1.62: 3825
        1.62 -     1.81: 56
  Bond restraints: 12850
  Sorted by residual:
  bond pdb=" N   SER A  52 "
       pdb=" CA  SER A  52 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   SER A  52 "
       pdb=" H   SER A  52 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" CB  VAL A 752 "
       pdb=" CG2 VAL A 752 "
    ideal  model  delta    sigma   weight residual
    1.521  1.558 -0.037 3.30e-02 9.18e+02 1.29e+00
  bond pdb=" CB  GLU A  97 "
       pdb=" CG  GLU A  97 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.18e-01
  bond pdb=" CA  ILE A 775 "
       pdb=" CB  ILE A 775 "
    ideal  model  delta    sigma   weight residual
    1.540  1.527  0.013 1.36e-02 5.41e+03 9.15e-01
  ... (remaining 12845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.72: 23234
        6.72 -    13.45: 2
       13.45 -    20.17: 0
       20.17 -    26.90: 0
       26.90 -    33.62: 3
  Bond angle restraints: 23239
  Sorted by residual:
  angle pdb=" N9    A T  32 "
        pdb=" C1'   A T  32 "
        pdb=" H1'   A T  32 "
      ideal   model   delta    sigma   weight residual
     109.00   75.38   33.62 3.00e+00 1.11e-01 1.26e+02
  angle pdb=" C2'   A T  32 "
        pdb=" C1'   A T  32 "
        pdb=" H1'   A T  32 "
      ideal   model   delta    sigma   weight residual
     109.00   79.75   29.25 3.00e+00 1.11e-01 9.51e+01
  angle pdb=" O4'   A T  32 "
        pdb=" C1'   A T  32 "
        pdb=" H1'   A T  32 "
      ideal   model   delta    sigma   weight residual
     109.00   80.73   28.27 3.00e+00 1.11e-01 8.88e+01
  angle pdb=" C2'   A T  32 "
        pdb=" C1'   A T  32 "
        pdb=" N9    A T  32 "
      ideal   model   delta    sigma   weight residual
     112.00  121.10   -9.10 1.50e+00 4.44e-01 3.68e+01
  angle pdb=" O4'   A T  32 "
        pdb=" C1'   A T  32 "
        pdb=" N9    A T  32 "
      ideal   model   delta    sigma   weight residual
     108.50  117.34   -8.84 1.50e+00 4.44e-01 3.48e+01
  ... (remaining 23234 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.57: 5584
       22.57 -    45.14: 354
       45.14 -    67.70: 163
       67.70 -    90.27: 25
       90.27 -   112.84: 5
  Dihedral angle restraints: 6131
    sinusoidal: 3887
      harmonic: 2244
  Sorted by residual:
  dihedral pdb=" O4'   U T  37 "
           pdb=" C1'   U T  37 "
           pdb=" N1    U T  37 "
           pdb=" C2    U T  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   87.16  112.84     1      1.50e+01 4.44e-03 5.92e+01
  dihedral pdb=" O4'   C T  36 "
           pdb=" C1'   C T  36 "
           pdb=" N1    C T  36 "
           pdb=" C2    C T  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -75.91  -84.09     1      1.50e+01 4.44e-03 3.83e+01
  dihedral pdb=" O4'   U T  60 "
           pdb=" C1'   U T  60 "
           pdb=" N1    U T  60 "
           pdb=" C2    U T  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -88.53  -71.47     1      1.50e+01 4.44e-03 2.91e+01
  ... (remaining 6128 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.176: 1146
       0.176 -    0.353: 1
       0.353 -    0.529: 0
       0.529 -    0.706: 0
       0.706 -    0.882: 1
  Chirality restraints: 1148
  Sorted by residual:
  chirality pdb=" C1'   A T  32 "
            pdb=" O4'   A T  32 "
            pdb=" C2'   A T  32 "
            pdb=" N9    A T  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    1.58    0.88 2.00e-01 2.50e+01 1.95e+01
  chirality pdb=" CB  VAL A 752 "
            pdb=" CA  VAL A 752 "
            pdb=" CG1 VAL A 752 "
            pdb=" CG2 VAL A 752 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  ... (remaining 1145 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 764 "    0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO A 765 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 765 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 765 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 480 "   -0.025 5.00e-02 4.00e+02   3.76e-02 2.27e+00
        pdb=" N   PRO A 481 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 481 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 481 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C T  36 "    0.005 2.00e-02 2.50e+03   7.67e-03 1.62e+00
        pdb=" N1    C T  36 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    C T  36 "    0.017 2.00e-02 2.50e+03
        pdb=" O2    C T  36 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3    C T  36 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4    C T  36 "    0.006 2.00e-02 2.50e+03
        pdb=" N4    C T  36 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    C T  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C T  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" H5    C T  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" H6    C T  36 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 209
        2.09 -     2.72: 19807
        2.72 -     3.34: 34386
        3.34 -     3.97: 42567
        3.97 -     4.60: 65642
  Nonbonded interactions: 162611
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 372 "
            pdb=" H   GLU A 372 "
     model   vdw
     1.460 2.450
  nonbonded pdb=" H   GLY A 489 "
            pdb=" O   ASN A 498 "
     model   vdw
     1.638 2.450
  nonbonded pdb=" OG  SER A 376 "
            pdb=" H   VAL A 377 "
     model   vdw
     1.638 2.450
  nonbonded pdb=" O   ASP A 106 "
            pdb=" H   VAL A 137 "
     model   vdw
     1.665 2.450
  nonbonded pdb=" OE1 GLU A 172 "
            pdb=" H   GLU A 172 "
     model   vdw
     1.666 2.450
  ... (remaining 162606 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.540
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     40.310
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:             0.020
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5851
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      :  0.002   0.037   6916  Z= 0.123
  Angle     :  0.516   9.100   9695  Z= 0.278
  Chirality :  0.044   0.882   1148
  Planarity :  0.003   0.040   1002
  Dihedral  : 18.285 112.840   2989
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.32 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.35), residues: 658
  helix:  1.56 (0.43), residues: 176
  sheet:  0.37 (0.48), residues: 128
  loop : -0.64 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 357 
 HIS   0.004   0.001   HIS A 527 
 PHE   0.007   0.001   PHE A 543 
 TYR   0.017   0.001   TYR A 354 
 ARG   0.001   0.000   ARG A 360 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  583 GLN cc_start: 0.7384 (mp10) cc_final: 0.7038 (pp30)
REVERT: A  663 TYR cc_start: 0.8016 (t80) cc_final: 0.7623 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.4182
  time to fit residues: 67.1035
Evaluate side-chains
  107 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0570
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   overall best weight:    2.3702

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 114 HIS
A 342 HIS
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.132864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.112630 restraints weight = 79192.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.116973 restraints weight = 42575.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.119829 restraints weight = 26623.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6916  Z= 0.200
  Angle     :  0.561   9.062   9695  Z= 0.295
  Chirality :  0.045   0.881   1148
  Planarity :  0.004   0.046   1002
  Dihedral  : 18.992 118.236   1718
  Min Nonbonded Distance : 1.723

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.38 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.44 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.12 (0.34), residues: 658
  helix:  1.25 (0.41), residues: 186
  sheet: -0.09 (0.47), residues: 131
  loop : -0.80 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 357 
 HIS   0.006   0.001   HIS A 114 
 PHE   0.012   0.001   PHE A 521 
 TYR   0.012   0.001   TYR A 354 
 ARG   0.006   0.000   ARG A 428 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  583 GLN cc_start: 0.7832 (mp10) cc_final: 0.7160 (pp30)
REVERT: A  663 TYR cc_start: 0.8692 (t80) cc_final: 0.8125 (t80)
REVERT: A  743 VAL cc_start: 0.8786 (m) cc_final: 0.8567 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.3904
  time to fit residues: 65.5709
Evaluate side-chains
  114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    0.0670
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 23 optimal weight:    0.2980
   chunk 33 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.7722

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 GLN
** A 749 HIS ** 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 = 0.4372 r_free = 0.4372 target = 0.134637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.114828 restraints weight = 80016.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.119264 restraints weight = 42523.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.122096 restraints weight = 26349.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6288
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6916  Z= 0.135
  Angle     :  0.510   9.073   9695  Z= 0.266
  Chirality :  0.044   0.884   1148
  Planarity :  0.004   0.048   1002
  Dihedral  : 18.956 118.682   1718
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.53 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.10 (0.34), residues: 658
  helix:  1.39 (0.42), residues: 186
  sheet: -0.03 (0.46), residues: 130
  loop : -0.90 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 357 
 HIS   0.005   0.001   HIS A 527 
 PHE   0.009   0.001   PHE A 109 
 TYR   0.010   0.001   TYR A 354 
 ARG   0.003   0.000   ARG A 623 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  583 GLN cc_start: 0.7827 (mp10) cc_final: 0.7052 (pp30)
REVERT: A  663 TYR cc_start: 0.8576 (t80) cc_final: 0.8006 (t80)
REVERT: A  743 VAL cc_start: 0.8794 (m) cc_final: 0.8573 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.3861
  time to fit residues: 63.7476
Evaluate side-chains
  117 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 67 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  56 ASN
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 727 GLN ** 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 = 0.4234 r_free = 0.4234 target = 0.123283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.103961 restraints weight = 83118.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.107839 restraints weight = 44402.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.110495 restraints weight = 28133.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6625
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   6916  Z= 0.298
  Angle     :  0.673   9.063   9695  Z= 0.355
  Chirality :  0.047   0.886   1148
  Planarity :  0.004   0.031   1002
  Dihedral  : 19.656 128.010   1718
  Min Nonbonded Distance : 1.725

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.51 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.18 (0.32), residues: 658
  helix:  0.02 (0.37), residues: 201
  sheet: -0.58 (0.46), residues: 130
  loop : -1.34 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 357 
 HIS   0.008   0.002   HIS A 724 
 PHE   0.017   0.002   PHE A 243 
 TYR   0.014   0.002   TYR A 329 
 ARG   0.010   0.001   ARG A 623 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 MET cc_start: 0.5955 (mpp) cc_final: 0.5196 (mmt)
REVERT: A  663 TYR cc_start: 0.8583 (t80) cc_final: 0.8194 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.3683
  time to fit residues: 57.5438
Evaluate side-chains
  107 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 45 optimal weight:    0.0770
   chunk 42 optimal weight:   10.0000
   chunk 59 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    3.8144

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 327 GLN
A 457 GLN
** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.121959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.105253 restraints weight = 96877.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.108538 restraints weight = 55142.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.110759 restraints weight = 36568.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6916  Z= 0.260
  Angle     :  0.637   9.108   9695  Z= 0.337
  Chirality :  0.046   0.894   1148
  Planarity :  0.005   0.055   1002
  Dihedral  : 19.911 128.531   1718
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.51 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.54 (0.32), residues: 658
  helix: -0.05 (0.37), residues: 200
  sheet: -0.84 (0.47), residues: 122
  loop : -1.70 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 587 
 HIS   0.009   0.002   HIS A 724 
 PHE   0.022   0.002   PHE A  80 
 TYR   0.022   0.002   TYR A  75 
 ARG   0.005   0.001   ARG A 623 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 MET cc_start: 0.5958 (mpp) cc_final: 0.5169 (mmt)
REVERT: A  583 GLN cc_start: 0.7823 (mp10) cc_final: 0.7092 (pp30)
REVERT: A  637 PHE cc_start: 0.7585 (t80) cc_final: 0.7177 (t80)
REVERT: A  663 TYR cc_start: 0.8618 (t80) cc_final: 0.8226 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.3700
  time to fit residues: 55.2865
Evaluate side-chains
  102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.122501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.102680 restraints weight = 80579.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.106683 restraints weight = 42920.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.109388 restraints weight = 27463.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6916  Z= 0.165
  Angle     :  0.570   9.117   9695  Z= 0.298
  Chirality :  0.045   0.894   1148
  Planarity :  0.004   0.045   1002
  Dihedral  : 19.783 127.949   1718
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.05 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.43 (0.32), residues: 658
  helix:  0.05 (0.37), residues: 206
  sheet: -0.85 (0.48), residues: 119
  loop : -1.64 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 587 
 HIS   0.005   0.001   HIS A  98 
 PHE   0.007   0.001   PHE A 725 
 TYR   0.009   0.001   TYR A 354 
 ARG   0.002   0.000   ARG A 428 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 MET cc_start: 0.5937 (mpp) cc_final: 0.5195 (mmt)
REVERT: A  637 PHE cc_start: 0.7404 (t80) cc_final: 0.7036 (t80)
REVERT: A  663 TYR cc_start: 0.8506 (t80) cc_final: 0.8131 (t80)
REVERT: A  685 HIS cc_start: 0.7161 (t-90) cc_final: 0.6908 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.4138
  time to fit residues: 64.0229
Evaluate side-chains
  101 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 42 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 390 ASN
** A 457 GLN ** 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 = 0.4259 r_free = 0.4259 target = 0.124427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.104460 restraints weight = 78667.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.108487 restraints weight = 42336.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.111154 restraints weight = 27230.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6611
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6916  Z= 0.144
  Angle     :  0.538   9.158   9695  Z= 0.280
  Chirality :  0.045   0.893   1148
  Planarity :  0.004   0.045   1002
  Dihedral  : 19.665 127.066   1718
  Min Nonbonded Distance : 1.822

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.05 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.19 (0.32), residues: 658
  helix:  0.35 (0.38), residues: 206
  sheet: -0.79 (0.47), residues: 124
  loop : -1.52 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 115 
 HIS   0.005   0.001   HIS A  98 
 PHE   0.007   0.001   PHE A 456 
 TYR   0.022   0.002   TYR A 329 
 ARG   0.002   0.000   ARG A 534 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 MET cc_start: 0.5955 (mpp) cc_final: 0.5232 (mmt)
REVERT: A  637 PHE cc_start: 0.7480 (t80) cc_final: 0.7138 (t80)
REVERT: A  663 TYR cc_start: 0.8538 (t80) cc_final: 0.8184 (t80)
REVERT: A  685 HIS cc_start: 0.7238 (t-90) cc_final: 0.7000 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.3958
  time to fit residues: 59.7970
Evaluate side-chains
  107 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 69 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 457 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.122393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.102576 restraints weight = 80099.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.106645 restraints weight = 42888.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.109371 restraints weight = 27386.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6650
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6916  Z= 0.172
  Angle     :  0.556   9.148   9695  Z= 0.292
  Chirality :  0.045   0.891   1148
  Planarity :  0.004   0.038   1002
  Dihedral  : 19.746 127.252   1718
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.81 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.28 (0.32), residues: 658
  helix:  0.30 (0.38), residues: 200
  sheet: -0.88 (0.47), residues: 124
  loop : -1.55 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 115 
 HIS   0.005   0.001   HIS A  98 
 PHE   0.010   0.001   PHE A 725 
 TYR   0.020   0.002   TYR A 329 
 ARG   0.003   0.000   ARG A 428 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 MET cc_start: 0.6043 (mpp) cc_final: 0.5315 (mmt)
REVERT: A  663 TYR cc_start: 0.8563 (t80) cc_final: 0.8227 (t80)
REVERT: A  685 HIS cc_start: 0.7254 (t-90) cc_final: 0.6995 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.3729
  time to fit residues: 54.2269
Evaluate side-chains
  102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 52 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 583 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.124015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.103646 restraints weight = 77267.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.107851 restraints weight = 40939.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.110652 restraints weight = 26036.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6916  Z= 0.140
  Angle     :  0.537   9.147   9695  Z= 0.279
  Chirality :  0.045   0.891   1148
  Planarity :  0.004   0.038   1002
  Dihedral  : 19.661 127.876   1718
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  7.14 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.22 (0.32), residues: 658
  helix:  0.35 (0.38), residues: 202
  sheet: -0.89 (0.46), residues: 130
  loop : -1.51 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.005   0.001   HIS A  98 
 PHE   0.007   0.001   PHE A 725 
 TYR   0.019   0.001   TYR A 329 
 ARG   0.002   0.000   ARG A 428 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  583 GLN cc_start: 0.8998 (mm110) cc_final: 0.8233 (mp10)
REVERT: A  626 SER cc_start: 0.9358 (m) cc_final: 0.9117 (p)
REVERT: A  663 TYR cc_start: 0.8518 (t80) cc_final: 0.8186 (t80)
REVERT: A  685 HIS cc_start: 0.7223 (t-90) cc_final: 0.6976 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.3665
  time to fit residues: 55.5649
Evaluate side-chains
  105 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0070
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   overall best weight:    2.8006

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 327 GLN
** A 727 GLN ** 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 = 0.4196 r_free = 0.4196 target = 0.120281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.101029 restraints weight = 81576.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.104940 restraints weight = 43721.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.107618 restraints weight = 27915.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.4919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6916  Z= 0.229
  Angle     :  0.592   9.127   9695  Z= 0.313
  Chirality :  0.046   0.890   1148
  Planarity :  0.004   0.034   1002
  Dihedral  : 19.981 129.968   1718
  Min Nonbonded Distance : 1.757

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  9.57 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.52 (0.32), residues: 658
  helix: -0.02 (0.37), residues: 206
  sheet: -1.16 (0.46), residues: 130
  loop : -1.56 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 587 
 HIS   0.006   0.001   HIS A 724 
 PHE   0.013   0.002   PHE A 521 
 TYR   0.028   0.002   TYR A 354 
 ARG   0.004   0.000   ARG A 428 

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 MET cc_start: 0.6179 (mpp) cc_final: 0.5417 (mmt)
REVERT: A  663 TYR cc_start: 0.8605 (t80) cc_final: 0.8313 (t80)
REVERT: A  685 HIS cc_start: 0.7300 (t-90) cc_final: 0.7014 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.3779
  time to fit residues: 57.3069
Evaluate side-chains
  101 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 33 optimal weight:    8.9990
   chunk 27 optimal weight:    0.4980
   chunk 55 optimal weight:   10.0000
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 327 GLN
** A 727 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.118325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.099105 restraints weight = 82443.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.102833 restraints weight = 43835.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.105421 restraints weight = 28642.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.5446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6916  Z= 0.230
  Angle     :  0.614   9.099   9695  Z= 0.324
  Chirality :  0.047   0.893   1148
  Planarity :  0.004   0.033   1002
  Dihedral  : 20.275 135.852   1718
  Min Nonbonded Distance : 1.753

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 10.03 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.72 (0.32), residues: 658
  helix: -0.28 (0.36), residues: 207
  sheet: -1.31 (0.46), residues: 130
  loop : -1.60 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 115 
 HIS   0.009   0.001   HIS A 342 
 PHE   0.010   0.002   PHE A 521 
 TYR   0.018   0.002   TYR A 329 
 ARG   0.009   0.001   ARG A 353 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4683.73 seconds
wall clock time: 83 minutes 54.84 seconds (5034.84 seconds total)