Starting phenix.real_space_refine (version: dev)
on Sun Dec 11 16:57:20 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/12_2022/8b3j_15830.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/12_2022/8b3j_15830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/12_2022/8b3j_15830.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/12_2022/8b3j_15830.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/12_2022/8b3j_15830.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3j_15830/12_2022/8b3j_15830.pdb"
  }
  resolution = 3.1
  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=   0.032 sd=   0.161
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  661": "OE1" <-> "OE2"
    Residue "A GLU  799": "OE1" <-> "OE2"
    Residue "A GLU  823": "OE1" <-> "OE2"
    Residue "A GLU  825": "OE1" <-> "OE2"
    Residue "A ASP  853": "OD1" <-> "OD2"
    Residue "B ASP  255": "OD1" <-> "OD2"
    Residue "B GLU  274": "OE1" <-> "OE2"
    Residue "C GLU  396": "OE1" <-> "OE2"
    Residue "C PHE  468": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  489": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  504": "OD1" <-> "OD2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib"
  Total number of atoms: 5688
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2034
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 24, 'TRANS': 232}
    Chain: "B"
      Number of atoms: 1456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1456
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 12, 'TRANS': 170}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2198
          Classifications: {'peptide': 278}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 262}
  Time building chain proxies: 3.85, per 1000 atoms: 0.68
  Number of scatterers: 5688
  At special positions: 0
  Unit cell: (108.9, 101.2, 93.5, 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    1057      8.00
     N     976      7.00
     C    3635      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: 2.03
  Conformation dependent library (CDL) restraints added in 858.8 milliseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1326

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 11 sheets defined
      9.1% alpha, 29.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 665 through 670
    Processing helix  chain 'A' and resid 683 through 687
      removed outlier: 3.750A  pdb=" N   THR A 686 " --> pdb=" O   THR A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 736
    Processing helix  chain 'A' and resid 796 through 802
      removed outlier: 3.636A  pdb=" N   GLN A 802 " --> pdb=" O   THR A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 846
    Processing helix  chain 'B' and resid 112 through 119
    Processing helix  chain 'B' and resid 173 through 182
      removed outlier: 3.678A  pdb=" N   THR B 179 " --> pdb=" O   GLY B 175 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   MET B 180 " --> pdb=" O   HIS B 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 379
    Processing helix  chain 'C' and resid 388 through 392
    Processing helix  chain 'C' and resid 441 through 447
      removed outlier: 3.520A  pdb=" N   ALA C 446 " --> pdb=" O   PRO C 442 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR C 447 " --> pdb=" O   VAL C 443 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 640 through 641
      removed outlier: 4.295A  pdb=" N   ASP C 400 " --> pdb=" O   TRP C 580 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL C 582 " --> pdb=" O   TYR C 398 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   TYR C 398 " --> pdb=" O   VAL C 582 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 674 through 678
      removed outlier: 5.085A  pdb=" N   ALA A 870 " --> pdb=" O   TYR A 676 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   ALA A 678 " --> pdb=" O   TRP A 868 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   TRP A 868 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 753 " --> pdb=" O   ALA A 867 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ARG A 747 " --> pdb=" O   ALA A 873 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ASP C 361 " --> pdb=" O   GLU A 823 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 783 through 788
      removed outlier: 4.470A  pdb=" N   ARG A 849 " --> pdb=" O   VAL A 772 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL A 772 " --> pdb=" O   ARG A 849 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 766 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 742 through 743
    Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 891
    Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 101
      removed outlier: 5.474A  pdb=" N   ARG B  95 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ALA B 252 " --> pdb=" O   ARG B  95 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   MET B  97 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   THR B 247 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   VAL B 257 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ARG B 134 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   LEU B 259 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   TYR B 132 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLY B 197 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 101
      removed outlier: 5.474A  pdb=" N   ARG B  95 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ALA B 252 " --> pdb=" O   ARG B  95 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   MET B  97 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   THR B 247 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   VAL B 257 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ARG B 134 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   LEU B 259 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   TYR B 132 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111
      removed outlier: 6.407A  pdb=" N   LYS B 152 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ALA B 232 " --> pdb=" O   TYR B 150 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   TYR B 150 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498
      removed outlier: 6.761A  pdb=" N   ARG C 470 " --> pdb=" O   ASP C 564 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ASP C 564 " --> pdb=" O   ARG C 470 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ARG C 472 " --> pdb=" O   VAL C 562 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   PHE C 415 " --> pdb=" O   VAL C 559 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL C 561 " --> pdb=" O   LEU C 413 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   LEU C 413 " --> pdb=" O   VAL C 561 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 427 through 428
      removed outlier: 3.613A  pdb=" N   GLY C 437 " --> pdb=" O   PHE C 427 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519

    149 hydrogen bonds defined for protein.
    381 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: 1.79

  Time building geometry restraints manager: 2.25 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: 1864
        1.34 -     1.46: 1073
        1.46 -     1.57: 2880
        1.57 -     1.69: 1
        1.69 -     1.80: 34
  Bond restraints: 5852
  Sorted by residual:
  bond pdb=" CA  GLU A 653 "
       pdb=" CB  GLU A 653 "
    ideal  model  delta    sigma   weight residual
    1.528  1.574 -0.046 2.61e-02 1.47e+03 3.05e+00
  bond pdb=" CG1 ILE A 697 "
       pdb=" CD1 ILE A 697 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.59e+00
  bond pdb=" C   LEU A 669 "
       pdb=" N   VAL A 670 "
    ideal  model  delta    sigma   weight residual
    1.338  1.328  0.010 1.01e-02 9.80e+03 9.95e-01
  bond pdb=" CB  GLU A 653 "
       pdb=" CG  GLU A 653 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.88e-01
  bond pdb=" CB  ASP A 703 "
       pdb=" CG  ASP A 703 "
    ideal  model  delta    sigma   weight residual
    1.516  1.495  0.021 2.50e-02 1.60e+03 7.23e-01
  ... (remaining 5847 not shown)

  Histogram of bond angle deviations from ideal:
       99.43 -   106.35: 232
      106.35 -   113.26: 3045
      113.26 -   120.18: 2038
      120.18 -   127.10: 2568
      127.10 -   134.01: 91
  Bond angle restraints: 7974
  Sorted by residual:
  angle pdb=" N   SER C 592 "
        pdb=" CA  SER C 592 "
        pdb=" C   SER C 592 "
      ideal   model   delta    sigma   weight residual
     110.24  114.72   -4.48 1.30e+00 5.92e-01 1.19e+01
  angle pdb=" C   ALA C 591 "
        pdb=" N   SER C 592 "
        pdb=" CA  SER C 592 "
      ideal   model   delta    sigma   weight residual
     120.82  125.31   -4.49 1.47e+00 4.63e-01 9.33e+00
  angle pdb=" CA  GLU A 653 "
        pdb=" CB  GLU A 653 "
        pdb=" CG  GLU A 653 "
      ideal   model   delta    sigma   weight residual
     114.10  119.16   -5.06 2.00e+00 2.50e-01 6.40e+00
  angle pdb=" CA  PRO A 820 "
        pdb=" C   PRO A 820 "
        pdb=" O   PRO A 820 "
      ideal   model   delta    sigma   weight residual
     121.38  119.45    1.93 7.70e-01 1.69e+00 6.28e+00
  angle pdb=" N   LEU B 230 "
        pdb=" CA  LEU B 230 "
        pdb=" C   LEU B 230 "
      ideal   model   delta    sigma   weight residual
     113.12  110.18    2.94 1.25e+00 6.40e-01 5.54e+00
  ... (remaining 7969 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 2980
       17.50 -    35.00: 359
       35.00 -    52.51: 83
       52.51 -    70.01: 12
       70.01 -    87.51: 3
  Dihedral angle restraints: 3437
    sinusoidal: 1367
      harmonic: 2070
  Sorted by residual:
  dihedral pdb=" CA  LEU A 880 "
           pdb=" C   LEU A 880 "
           pdb=" N   SER A 881 "
           pdb=" CA  SER A 881 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.71  -22.29     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  SER B 213 "
           pdb=" C   SER B 213 "
           pdb=" N   GLU B 214 "
           pdb=" CA  GLU B 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  LEU A 832 "
           pdb=" C   LEU A 832 "
           pdb=" N   ARG A 833 "
           pdb=" CA  ARG A 833 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.58  -20.42     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 3434 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 582
       0.041 -    0.081: 191
       0.081 -    0.121: 77
       0.121 -    0.162: 5
       0.162 -    0.202: 1
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CA  ILE A 697 "
            pdb=" N   ILE A 697 "
            pdb=" C   ILE A 697 "
            pdb=" CB  ILE A 697 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ILE B 248 "
            pdb=" N   ILE B 248 "
            pdb=" C   ILE B 248 "
            pdb=" CB  ILE B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  ILE C 475 "
            pdb=" N   ILE C 475 "
            pdb=" C   ILE C 475 "
            pdb=" CB  ILE C 475 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 853 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 714 "    0.025 5.00e-02 4.00e+02   3.78e-02 2.29e+00
        pdb=" N   PRO A 715 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 715 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 715 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 158 "   -0.024 5.00e-02 4.00e+02   3.61e-02 2.09e+00
        pdb=" N   PRO B 159 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 159 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 159 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 775 "   -0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO A 776 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 776 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 776 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 195
        2.70 -     3.25: 5010
        3.25 -     3.80: 7952
        3.80 -     4.35: 10703
        4.35 -     4.90: 18898
  Nonbonded interactions: 42758
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 145 "
            pdb=" OG  SER B 194 "
     model   vdw
     2.144 2.440
  nonbonded pdb=" OE1 GLU B 131 "
            pdb=" OG  SER B 213 "
     model   vdw
     2.162 2.440
  nonbonded pdb=" ND2 ASN A 796 "
            pdb=" OE1 GLU A 799 "
     model   vdw
     2.192 2.520
  nonbonded pdb=" OG  SER C 364 "
            pdb=" O   THR C 366 "
     model   vdw
     2.216 2.440
  nonbonded pdb=" N   GLU A 653 "
            pdb=" OE1 GLU A 653 "
     model   vdw
     2.222 2.520
  ... (remaining 42753 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    3635      2.51       5
     N     976      2.21       5
     O    1057      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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          8.990
  Check model and map are aligned:         0.090
  Convert atoms to be neutral:             0.060
  Process input model:                     20.000
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
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      :  0.005   0.049   5852  Z= 0.313
  Angle     :  0.630   6.597   7974  Z= 0.337
  Chirality :  0.046   0.202    856
  Planarity :  0.004   0.038   1048
  Dihedral  : 15.709  87.512   2111
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.49 (0.30), residues: 710
  helix: -2.08 (0.67), residues: 54
  sheet: -0.62 (0.37), residues: 194
  loop : -2.19 (0.27), residues: 462

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.696 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2226
  time to fit residues: 20.5475
Evaluate side-chains
  68 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.754 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9574
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 543 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.0567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5852  Z= 0.342
  Angle     :  0.618   7.091   7974  Z= 0.324
  Chirality :  0.047   0.183    856
  Planarity :  0.005   0.033   1048
  Dihedral  :  4.841  22.495    786
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer Outliers :  3.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.51 (0.30), residues: 710
  helix: -2.17 (0.61), residues: 60
  sheet: -0.65 (0.37), residues: 199
  loop : -2.18 (0.27), residues: 451

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.731 
Fit side-chains
  outliers start: 21
  outliers final: 11
  residues processed: 89
  average time/residue: 0.2102
  time to fit residues: 23.9402
Evaluate side-chains
  82 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.699 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1006
  time to fit residues: 2.5445
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 56 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 51 optimal weight:   30.0000
   chunk 62 optimal weight:    3.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
C 543 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.0700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5852  Z= 0.288
  Angle     :  0.585   6.698   7974  Z= 0.306
  Chirality :  0.046   0.169    856
  Planarity :  0.004   0.033   1048
  Dihedral  :  4.728  22.492    786
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer Outliers :  2.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.51 (0.30), residues: 710
  helix: -2.18 (0.62), residues: 60
  sheet: -0.62 (0.37), residues: 206
  loop : -2.23 (0.27), residues: 444

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.652 
Fit side-chains
  outliers start: 18
  outliers final: 6
  residues processed: 89
  average time/residue: 0.1972
  time to fit residues: 22.8907
Evaluate side-chains
  81 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.632 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0533
  time to fit residues: 1.4736
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 30 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
C 606 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.0873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.047   5852  Z= 0.395
  Angle     :  0.645   6.923   7974  Z= 0.338
  Chirality :  0.048   0.167    856
  Planarity :  0.005   0.039   1048
  Dihedral  :  4.945  23.376    786
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer Outliers :  3.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.55 (0.30), residues: 710
  helix: -2.36 (0.56), residues: 66
  sheet: -0.43 (0.38), residues: 197
  loop : -2.30 (0.27), residues: 447

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.677 
Fit side-chains
  outliers start: 21
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1913
  time to fit residues: 23.2831
Evaluate side-chains
  84 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.636 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0775
  time to fit residues: 2.3133
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 60 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   overall best weight:    5.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5852  Z= 0.281
  Angle     :  0.588   6.459   7974  Z= 0.308
  Chirality :  0.046   0.158    856
  Planarity :  0.004   0.032   1048
  Dihedral  :  4.750  22.892    786
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer Outliers :  1.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.48 (0.30), residues: 710
  helix: -2.27 (0.57), residues: 66
  sheet: -0.40 (0.37), residues: 197
  loop : -2.26 (0.27), residues: 447

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.646 
Fit side-chains
  outliers start: 10
  outliers final: 5
  residues processed: 77
  average time/residue: 0.2160
  time to fit residues: 21.3802
Evaluate side-chains
  68 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.707 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1626
  time to fit residues: 2.0127
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    4.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5852  Z= 0.245
  Angle     :  0.568   8.265   7974  Z= 0.296
  Chirality :  0.045   0.156    856
  Planarity :  0.004   0.031   1048
  Dihedral  :  4.573  22.411    786
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer Outliers :  1.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.47 (0.30), residues: 710
  helix: -2.21 (0.58), residues: 66
  sheet: -0.50 (0.37), residues: 206
  loop : -2.24 (0.27), residues: 438

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.721 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 72
  average time/residue: 0.2165
  time to fit residues: 20.2294
Evaluate side-chains
  70 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.700 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0568
  time to fit residues: 1.4578
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:   20.0000
   chunk 57 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 67 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 20 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    4.7388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5852  Z= 0.260
  Angle     :  0.574   7.079   7974  Z= 0.299
  Chirality :  0.045   0.154    856
  Planarity :  0.004   0.030   1048
  Dihedral  :  4.561  22.508    786
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer Outliers :  1.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.46 (0.30), residues: 710
  helix: -2.21 (0.58), residues: 66
  sheet: -0.48 (0.37), residues: 206
  loop : -2.23 (0.27), residues: 438

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.740 
Fit side-chains
  outliers start: 8
  outliers final: 2
  residues processed: 73
  average time/residue: 0.2127
  time to fit residues: 20.0522
Evaluate side-chains
  68 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.648 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0526
  time to fit residues: 1.0587
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 58 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 531 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5852  Z= 0.207
  Angle     :  0.554   6.647   7974  Z= 0.288
  Chirality :  0.044   0.152    856
  Planarity :  0.004   0.029   1048
  Dihedral  :  4.395  21.950    786
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer Outliers :  0.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.38 (0.30), residues: 710
  helix: -2.19 (0.58), residues: 66
  sheet: -0.43 (0.37), residues: 206
  loop : -2.16 (0.28), residues: 438

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.738 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 72
  average time/residue: 0.2426
  time to fit residues: 21.9455
Evaluate side-chains
  69 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.692 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0564
  time to fit residues: 1.1396
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 59 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   overall best weight:    4.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5852  Z= 0.237
  Angle     :  0.567   6.414   7974  Z= 0.296
  Chirality :  0.045   0.152    856
  Planarity :  0.004   0.029   1048
  Dihedral  :  4.427  22.557    786
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer Outliers :  0.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.32 (0.30), residues: 710
  helix: -1.98 (0.62), residues: 60
  sheet: -0.43 (0.37), residues: 206
  loop : -2.13 (0.27), residues: 444

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.703 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 66
  average time/residue: 0.2278
  time to fit residues: 19.2706
Evaluate side-chains
  65 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.686 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0947
  time to fit residues: 1.1019
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 64 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0980
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 17 optimal weight:   20.0000
   chunk 51 optimal weight:    0.0040
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.8196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5852  Z= 0.187
  Angle     :  0.543   6.371   7974  Z= 0.282
  Chirality :  0.044   0.154    856
  Planarity :  0.004   0.028   1048
  Dihedral  :  4.275  21.633    786
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer Outliers :  0.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.28 (0.30), residues: 710
  helix: -1.92 (0.63), residues: 60
  sheet: -0.54 (0.36), residues: 210
  loop : -2.04 (0.28), residues: 440

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.772 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 69
  average time/residue: 0.2220
  time to fit residues: 19.7583
Evaluate side-chains
  66 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.672 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0561
  time to fit residues: 1.1252
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 63 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    5.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.093791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.077449 restraints weight = 10085.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 2.28
r_work: 0.2856 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5852  Z= 0.309
  Angle     :  0.596   6.292   7974  Z= 0.313
  Chirality :  0.046   0.153    856
  Planarity :  0.005   0.077   1048
  Dihedral  :  4.625  22.647    786
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer Outliers :  0.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.31 (0.30), residues: 710
  helix: -2.03 (0.62), residues: 60
  sheet: -0.47 (0.37), residues: 208
  loop : -2.10 (0.28), residues: 442

===============================================================================
Job complete
usr+sys time: 1478.89 seconds
wall clock time: 27 minutes 9.14 seconds (1629.14 seconds total)