Starting phenix.real_space_refine (version: dev)
on Fri Feb 17 21:30:01 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/02_2023/6wu0_21901.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/02_2023/6wu0_21901.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/02_2023/6wu0_21901.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/02_2023/6wu0_21901.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/02_2023/6wu0_21901.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/02_2023/6wu0_21901.pdb"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.648
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
Process input model

  Symmetric amino acids flipped
    Residue "B ARG   15": "NH1" <-> "NH2"
    Residue "B ARG   16": "NH1" <-> "NH2"
    Residue "B TYR   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   52": "OD1" <-> "OD2"
    Residue "B ASP   64": "OD1" <-> "OD2"
    Residue "B ARG   98": "NH1" <-> "NH2"
    Residue "B GLU  127": "OE1" <-> "OE2"
    Residue "B ASP  129": "OD1" <-> "OD2"
    Residue "B ASP  191": "OD1" <-> "OD2"
    Residue "B PHE  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  227": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  251": "OE1" <-> "OE2"
    Residue "B ASP  267": "OD1" <-> "OD2"
    Residue "B GLU  268": "OE1" <-> "OE2"
    Residue "B PHE  270": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  297": "NH1" <-> "NH2"
    Residue "B ARG  300": "NH1" <-> "NH2"
    Residue "B ARG  359": "NH1" <-> "NH2"
    Residue "B TYR  397": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  448": "OD1" <-> "OD2"
    Residue "B ARG  476": "NH1" <-> "NH2"
    Residue "B PHE  477": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  479": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  486": "OD1" <-> "OD2"
    Residue "B GLU  490": "OE1" <-> "OE2"
    Residue "B ASP  500": "OD1" <-> "OD2"
    Residue "B ARG  558": "NH1" <-> "NH2"
    Residue "B TYR  595": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  660": "OD1" <-> "OD2"
    Residue "B ARG  690": "NH1" <-> "NH2"
    Residue "B ARG  718": "NH1" <-> "NH2"
    Residue "B PHE  742": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  744": "OD1" <-> "OD2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 6340
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 6340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 854, 6340
          Classifications: {'peptide': 854}
          Link IDs: {'PTRANS': 52, 'TRANS': 801}
          Chain breaks: 1
  Time building chain proxies: 4.16, per 1000 atoms: 0.66
  Number of scatterers: 6340
  At special positions: 0
  Unit cell: (89.64, 70.2, 131.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1133      8.00
     N    1097      7.00
     C    4090      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.63
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 1 sheets defined
      74.9% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1 through 15
    Processing helix  chain 'B' and resid 18 through 38
    Processing helix  chain 'B' and resid 52 through 66
      removed outlier: 3.538A  pdb=" N   LEU B  58 " --> pdb=" O   LYS B  54 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 70
      removed outlier: 3.711A  pdb=" N   ASN B  70 " --> pdb=" O   PRO B  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 67 through 70'
    Processing helix  chain 'B' and resid 81 through 102
      removed outlier: 4.036A  pdb=" N   ALA B 102 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 120
    Processing helix  chain 'B' and resid 126 through 140
    Processing helix  chain 'B' and resid 140 through 149
    Processing helix  chain 'B' and resid 152 through 171
      removed outlier: 4.107A  pdb=" N   VAL B 166 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
      Proline residue:  B 167  - end of helix
      removed outlier: 3.682A  pdb=" N   GLY B 171 " --> pdb=" O   PRO B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 177
    Processing helix  chain 'B' and resid 178 through 194
    Processing helix  chain 'B' and resid 233 through 247
      removed outlier: 4.156A  pdb=" N   ARG B 241 " --> pdb=" O   SER B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 253
    Processing helix  chain 'B' and resid 261 through 276
      removed outlier: 3.713A  pdb=" N   GLY B 276 " --> pdb=" O   SER B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 296
    Processing helix  chain 'B' and resid 298 through 324
      removed outlier: 3.543A  pdb=" N   ILE B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   SER B 304 " --> pdb=" O   ARG B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 332
      No H-bonds generated for 'chain 'B' and resid 330 through 332'
    Processing helix  chain 'B' and resid 333 through 342
      removed outlier: 4.315A  pdb=" N   VAL B 339 " --> pdb=" O   MET B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 360
      removed outlier: 4.239A  pdb=" N   ALA B 346 " --> pdb=" O   GLY B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 374
    Processing helix  chain 'B' and resid 375 through 391
    Processing helix  chain 'B' and resid 397 through 429
      removed outlier: 3.500A  pdb=" N   SER B 401 " --> pdb=" O   TYR B 397 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   LEU B 422 " --> pdb=" O   THR B 418 " (cutoff:3.500A)
      Proline residue:  B 423  - end of helix
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 3.805A  pdb=" N   TYR B 449 " --> pdb=" O   PRO B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 467
      removed outlier: 3.721A  pdb=" N   LEU B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA B 463 " --> pdb=" O   ILE B 459 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   GLY B 467 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 473
      removed outlier: 3.563A  pdb=" N   LEU B 471 " --> pdb=" O   ALA B 468 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA B 473 " --> pdb=" O   PRO B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.521A  pdb=" N   HIS B 483 " --> pdb=" O   ASN B 480 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS B 485 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 498
      removed outlier: 4.491A  pdb=" N   LEU B 495 " --> pdb=" O   SER B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 528
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 545 through 561
      removed outlier: 3.719A  pdb=" N   LYS B 549 " --> pdb=" O   ALA B 545 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY B 559 " --> pdb=" O   ALA B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 564
      No H-bonds generated for 'chain 'B' and resid 562 through 564'
    Processing helix  chain 'B' and resid 573 through 595
    Processing helix  chain 'B' and resid 599 through 614
      removed outlier: 3.539A  pdb=" N   ALA B 603 " --> pdb=" O   GLY B 599 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA B 614 " --> pdb=" O   LEU B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 644
      removed outlier: 3.538A  pdb=" N   GLU B 622 " --> pdb=" O   ALA B 618 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   VAL B 630 " --> pdb=" O   HIS B 626 " (cutoff:3.500A)
      Proline residue:  B 631  - end of helix
      removed outlier: 3.831A  pdb=" N   GLN B 644 " --> pdb=" O   ALA B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 649 through 653
    Processing helix  chain 'B' and resid 654 through 662
      removed outlier: 3.511A  pdb=" N   VAL B 658 " --> pdb=" O   PRO B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 699
      removed outlier: 3.671A  pdb=" N   LEU B 688 " --> pdb=" O   ASP B 684 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 708
    Processing helix  chain 'B' and resid 709 through 739
      removed outlier: 3.586A  pdb=" N   ALA B 713 " --> pdb=" O   ILE B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 741 through 767
      removed outlier: 4.126A  pdb=" N   VAL B 745 " --> pdb=" O   ARG B 741 " (cutoff:3.500A)
      Proline residue:  B 751  - end of helix
    Processing helix  chain 'B' and resid 776 through 796
      removed outlier: 3.887A  pdb=" N   MET B 794 " --> pdb=" O   VAL B 790 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 797 through 799
      No H-bonds generated for 'chain 'B' and resid 797 through 799'
    Processing helix  chain 'B' and resid 809 through 828
    Processing helix  chain 'B' and resid 831 through 854
      removed outlier: 4.311A  pdb=" N   MET B 837 " --> pdb=" O   GLY B 833 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE B 850 " --> pdb=" O   SER B 846 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 855 through 859
    Processing sheet with id=AA1, first strand: chain 'B' and resid 108 through 109
      removed outlier: 3.715A  pdb=" N   ALA B 215 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)

    436 hydrogen bonds defined for protein.
    1272 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2079
        1.34 -     1.46: 748
        1.46 -     1.57: 3601
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 6466
  Sorted by residual:
  bond pdb=" C   VAL B 858 "
       pdb=" O   VAL B 858 "
    ideal  model  delta    sigma   weight residual
    1.236  1.224  0.012 1.19e-02 7.06e+03 1.05e+00
  bond pdb=" CA  VAL B 670 "
       pdb=" CB  VAL B 670 "
    ideal  model  delta    sigma   weight residual
    1.533  1.545 -0.012 1.26e-02 6.30e+03 8.78e-01
  bond pdb=" CA  VAL B 858 "
       pdb=" C   VAL B 858 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.27e-02 6.20e+03 6.54e-01
  bond pdb=" C   GLU B 213 "
       pdb=" N   PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 2.34e-02 1.83e+03 5.68e-01
  bond pdb=" C   THR B 260 "
       pdb=" N   GLY B 261 "
    ideal  model  delta    sigma   weight residual
    1.331  1.320  0.011 1.46e-02 4.69e+03 5.56e-01
  ... (remaining 6461 not shown)

  Histogram of bond angle deviations from ideal:
      100.14 -   106.93: 247
      106.93 -   113.72: 3755
      113.72 -   120.51: 2631
      120.51 -   127.31: 2123
      127.31 -   134.10: 74
  Bond angle restraints: 8830
  Sorted by residual:
  angle pdb=" C   ASP B 665 "
        pdb=" N   GLY B 666 "
        pdb=" CA  GLY B 666 "
      ideal   model   delta    sigma   weight residual
     121.41  127.46   -6.05 1.96e+00 2.60e-01 9.51e+00
  angle pdb=" C   VAL B 750 "
        pdb=" CA  VAL B 750 "
        pdb=" CB  VAL B 750 "
      ideal   model   delta    sigma   weight residual
     113.70  110.92    2.78 9.50e-01 1.11e+00 8.54e+00
  angle pdb=" C   LEU B 749 "
        pdb=" N   VAL B 750 "
        pdb=" CA  VAL B 750 "
      ideal   model   delta    sigma   weight residual
     120.43  123.12   -2.69 9.60e-01 1.09e+00 7.83e+00
  angle pdb=" CA  LEU B 498 "
        pdb=" CB  LEU B 498 "
        pdb=" CG  LEU B 498 "
      ideal   model   delta    sigma   weight residual
     116.30  124.86   -8.56 3.50e+00 8.16e-02 5.98e+00
  angle pdb=" N   ARG B 740 "
        pdb=" CA  ARG B 740 "
        pdb=" C   ARG B 740 "
      ideal   model   delta    sigma   weight residual
     110.80  115.94   -5.14 2.13e+00 2.20e-01 5.83e+00
  ... (remaining 8825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 3480
       16.09 -    32.18: 328
       32.18 -    48.27: 80
       48.27 -    64.36: 13
       64.36 -    80.45: 3
  Dihedral angle restraints: 3904
    sinusoidal: 1447
      harmonic: 2457
  Sorted by residual:
  dihedral pdb=" CA  GLY B 666 "
           pdb=" C   GLY B 666 "
           pdb=" N   ARG B 667 "
           pdb=" CA  ARG B 667 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.88  -25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  ARG B 667 "
           pdb=" C   ARG B 667 "
           pdb=" N   ALA B 668 "
           pdb=" CA  ALA B 668 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.48  -20.52     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  LEU B 739 "
           pdb=" C   LEU B 739 "
           pdb=" N   ARG B 740 "
           pdb=" CA  ARG B 740 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.17  -18.83     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 3901 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 836
       0.045 -    0.090: 197
       0.090 -    0.134: 54
       0.134 -    0.179: 0
       0.179 -    0.224: 1
  Chirality restraints: 1088
  Sorted by residual:
  chirality pdb=" CB  ILE B 662 "
            pdb=" CA  ILE B 662 "
            pdb=" CG1 ILE B 662 "
            pdb=" CG2 ILE B 662 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CG  LEU B 804 "
            pdb=" CB  LEU B 804 "
            pdb=" CD1 LEU B 804 "
            pdb=" CD2 LEU B 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CA  ILE B 542 "
            pdb=" N   ILE B 542 "
            pdb=" C   ILE B 542 "
            pdb=" CB  ILE B 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1085 not shown)

  Planarity restraints: 1123
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 572 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO B 573 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 573 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 573 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 440 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.43e+00
        pdb=" N   PRO B 441 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 441 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 441 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 513 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.76e+00
        pdb=" N   PRO B 514 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 514 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 514 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1120 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 799
        2.75 -     3.29: 6708
        3.29 -     3.82: 10517
        3.82 -     4.36: 11236
        4.36 -     4.90: 19392
  Nonbonded interactions: 48652
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 167 "
            pdb=" OG  SER B 170 "
     model   vdw
     2.211 2.440
  nonbonded pdb=" OG  SER B 829 "
            pdb=" OG1 THR B 834 "
     model   vdw
     2.256 2.440
  nonbonded pdb=" O   PHE B 392 "
            pdb=" OG1 THR B 395 "
     model   vdw
     2.261 2.440
  nonbonded pdb=" O   ARG B  98 "
            pdb=" NH1 ARG B  98 "
     model   vdw
     2.291 2.520
  nonbonded pdb=" O   PRO B 151 "
            pdb=" OG  SER B 629 "
     model   vdw
     2.298 2.440
  ... (remaining 48647 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    4090      2.51       5
     N    1097      2.21       5
     O    1133      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:             0.520
  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:          0.330
  Check model and map are aligned:         0.100
  Process input model:                     21.840
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Set scattering table:                    0.070
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6276
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   0.023   6466  Z= 0.170
  Angle     :  0.647   8.562   8830  Z= 0.342
  Chirality :  0.040   0.224   1088
  Planarity :  0.004   0.040   1123
  Dihedral  : 13.427  80.447   2308
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer Outliers :  0.00 %
  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: -1.89 (0.27), residues: 850
  helix: -0.45 (0.20), residues: 562
  sheet: -1.69 (0.88), residues: 38
  loop : -2.89 (0.41), residues: 250

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1934
  time to fit residues: 38.3270
Evaluate side-chains
  125 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.714 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0067
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 25 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 ASN
B 222 GLN
B 474 HIS
B 483 HIS
B 548 GLN
B 656 GLN
B 722 GLN
B 831 HIS
B 856 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6466  Z= 0.238
  Angle     :  0.684   7.723   8830  Z= 0.339
  Chirality :  0.043   0.183   1088
  Planarity :  0.005   0.066   1123
  Dihedral  :  4.405  25.224    906
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer Outliers :  2.90 %
  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: -0.88 (0.29), residues: 850
  helix:  0.37 (0.21), residues: 588
  sheet: -1.08 (0.92), residues: 38
  loop : -3.01 (0.41), residues: 224

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1812
  time to fit residues: 32.9768
Evaluate side-chains
  131 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.732 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0634
  time to fit residues: 2.1737
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6466  Z= 0.255
  Angle     :  0.699   7.909   8830  Z= 0.345
  Chirality :  0.043   0.150   1088
  Planarity :  0.005   0.055   1123
  Dihedral  :  4.555  26.350    906
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer Outliers :  3.96 %
  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: -0.58 (0.29), residues: 850
  helix:  0.62 (0.21), residues: 582
  sheet: -0.95 (0.91), residues: 38
  loop : -2.86 (0.41), residues: 230

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 11
  residues processed: 142
  average time/residue: 0.1825
  time to fit residues: 35.5721
Evaluate side-chains
  131 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.624 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0692
  time to fit residues: 2.3692
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0370
   chunk 68 optimal weight:    9.9990
   overall best weight:    1.9864

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6340
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6466  Z= 0.175
  Angle     :  0.657   7.914   8830  Z= 0.316
  Chirality :  0.041   0.160   1088
  Planarity :  0.005   0.047   1123
  Dihedral  :  4.329  24.703    906
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer Outliers :  2.29 %
  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: -0.06 (0.30), residues: 850
  helix:  1.01 (0.22), residues: 579
  sheet: -0.64 (0.93), residues: 38
  loop : -2.67 (0.41), residues: 233

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 5
  residues processed: 133
  average time/residue: 0.1811
  time to fit residues: 32.6567
Evaluate side-chains
  131 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.635 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0626
  time to fit residues: 1.4921
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:   30.0000
   chunk 1 optimal weight:    0.0870
   chunk 61 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 56 optimal weight:    0.0010
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0670
   chunk 27 optimal weight:   30.0000
   overall best weight:    0.4304

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 222 GLN
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 HIS
B 656 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6258
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6466  Z= 0.167
  Angle     :  0.635   8.161   8830  Z= 0.305
  Chirality :  0.040   0.161   1088
  Planarity :  0.004   0.040   1123
  Dihedral  :  4.196  24.264    906
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer Outliers :  2.59 %
  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:  0.42 (0.30), residues: 850
  helix:  1.33 (0.22), residues: 575
  sheet: -0.32 (0.94), residues: 38
  loop : -2.29 (0.42), residues: 237

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 6
  residues processed: 140
  average time/residue: 0.1779
  time to fit residues: 33.7600
Evaluate side-chains
  134 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.652 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1373
  time to fit residues: 2.1305
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0470
   chunk 48 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 27 optimal weight:   40.0000
   chunk 43 optimal weight:   20.0000
   chunk 79 optimal weight:    0.7980
   overall best weight:    3.7684

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

Flipped N/Q/H residues before XYZ refinement:
B 274 GLN
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 566 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6361
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6466  Z= 0.224
  Angle     :  0.693   8.634   8830  Z= 0.334
  Chirality :  0.043   0.150   1088
  Planarity :  0.005   0.042   1123
  Dihedral  :  4.345  27.284    906
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer Outliers :  2.44 %
  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:  0.38 (0.30), residues: 850
  helix:  1.40 (0.22), residues: 561
  sheet: -0.54 (0.92), residues: 38
  loop : -2.35 (0.40), residues: 251

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 11
  residues processed: 132
  average time/residue: 0.1743
  time to fit residues: 31.3403
Evaluate side-chains
  136 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.706 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0649
  time to fit residues: 2.2952
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 45 optimal weight:    0.2980
   chunk 81 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6313
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6466  Z= 0.182
  Angle     :  0.667   7.711   8830  Z= 0.322
  Chirality :  0.041   0.160   1088
  Planarity :  0.005   0.041   1123
  Dihedral  :  4.305  25.362    906
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer Outliers :  1.68 %
  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:  0.51 (0.30), residues: 850
  helix:  1.47 (0.22), residues: 569
  sheet: -0.42 (0.92), residues: 38
  loop : -2.34 (0.41), residues: 243

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 4
  residues processed: 135
  average time/residue: 0.1740
  time to fit residues: 32.2886
Evaluate side-chains
  129 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.715 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0634
  time to fit residues: 1.4828
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:   30.0000
   chunk 24 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0000
   chunk 40 optimal weight:   20.0000
   chunk 7 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6466  Z= 0.205
  Angle     :  0.692   9.117   8830  Z= 0.336
  Chirality :  0.042   0.216   1088
  Planarity :  0.005   0.042   1123
  Dihedral  :  4.381  26.200    906
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer Outliers :  2.13 %
  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:  0.43 (0.30), residues: 850
  helix:  1.38 (0.22), residues: 567
  sheet: -0.55 (0.90), residues: 38
  loop : -2.26 (0.41), residues: 245

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 6
  residues processed: 134
  average time/residue: 0.1801
  time to fit residues: 32.7327
Evaluate side-chains
  130 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.707 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0669
  time to fit residues: 1.8316
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 68 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 644 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6466  Z= 0.239
  Angle     :  0.732   9.186   8830  Z= 0.356
  Chirality :  0.043   0.184   1088
  Planarity :  0.005   0.044   1123
  Dihedral  :  4.549  28.396    906
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer Outliers :  1.07 %
  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:  0.32 (0.30), residues: 850
  helix:  1.25 (0.22), residues: 572
  sheet: -0.69 (0.89), residues: 38
  loop : -2.21 (0.42), residues: 240

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 128
  average time/residue: 0.1809
  time to fit residues: 31.3861
Evaluate side-chains
  124 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.730 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0631
  time to fit residues: 1.4843
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:   40.0000
   chunk 84 optimal weight:    0.2980
   chunk 77 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0010
   chunk 7 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    3.2592

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

Flipped N/Q/H residues before XYZ refinement:
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6466  Z= 0.222
  Angle     :  0.744   9.595   8830  Z= 0.361
  Chirality :  0.043   0.175   1088
  Planarity :  0.005   0.047   1123
  Dihedral  :  4.560  26.765    906
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer Outliers :  0.15 %
  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:  0.21 (0.30), residues: 850
  helix:  1.18 (0.22), residues: 577
  sheet: -0.70 (0.87), residues: 38
  loop : -2.38 (0.42), residues: 235

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1798
  time to fit residues: 30.8141
Evaluate side-chains
  122 residues out of total 656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.693 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0286
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 67 optimal weight:   20.0000
   chunk 28 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 59 optimal weight:   40.0000
   chunk 3 optimal weight:    7.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.227217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.205065 restraints weight = 9083.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.209518 restraints weight = 5403.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.212619 restraints weight = 3593.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6426
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6466  Z= 0.259
  Angle     :  0.786   9.677   8830  Z= 0.383
  Chirality :  0.044   0.181   1088
  Planarity :  0.006   0.047   1123
  Dihedral  :  4.715  28.855    906
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer Outliers :  0.76 %
  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: -0.04 (0.30), residues: 850
  helix:  0.92 (0.22), residues: 588
  sheet: -1.03 (0.84), residues: 38
  loop : -2.35 (0.44), residues: 224

===============================================================================
Job complete
usr+sys time: 1423.41 seconds
wall clock time: 26 minutes 47.53 seconds (1607.53 seconds total)