Starting phenix.real_space_refine
on Fri Jul 19 11:00:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9i_36987/07_2024/8k9i_36987.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9i_36987/07_2024/8k9i_36987.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9i_36987/07_2024/8k9i_36987.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9i_36987/07_2024/8k9i_36987.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9i_36987/07_2024/8k9i_36987.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9i_36987/07_2024/8k9i_36987.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    4850      2.51       5
     N    1340      2.21       5
     O    1410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C GLU   55": "OE1" <-> "OE2"
    Residue "C GLU   56": "OE1" <-> "OE2"
    Residue "C TYR   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   79": "OE1" <-> "OE2"
    Residue "C GLU  137": "OE1" <-> "OE2"
    Residue "C PHE  147": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  216": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  258": "OE1" <-> "OE2"
    Residue "C GLU  267": "OE1" <-> "OE2"
    Residue "C GLU  315": "OE1" <-> "OE2"
    Residue "C GLU  323": "OE1" <-> "OE2"
    Residue "C TYR  341": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  428": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  432": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  611": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  613": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K GLU   62": "OE1" <-> "OE2"
    Residue "L PHE   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 7657
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 5712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 694, 5712
          Classifications: {'peptide': 694}
          Link IDs: {'PTRANS': 15, 'TRANS': 678}
          Chain breaks: 10
    Chain: "K"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 873
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 5
    Chain: "L"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 749
          Classifications: {'peptide': 95}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 92}
          Chain breaks: 6
    Chain: "R"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 323
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 1, 'TRANS': 37}
          Chain breaks: 4
  Time building chain proxies: 6.60, per 1000 atoms: 0.86
  Number of scatterers: 7657
  At special positions: 0
  Unit cell: (94.415, 88.668, 169.947, 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      57     16.00
     O    1410      8.00
     N    1340      7.00
     C    4850      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: 3.13
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1802

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 6 sheets defined
      67.7% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'C' and resid 26 through 46
    Processing helix  chain 'C' and resid 53 through 67
    Processing helix  chain 'C' and resid 69 through 88
    Processing helix  chain 'C' and resid 89 through 95
    Processing helix  chain 'C' and resid 100 through 121
    Processing helix  chain 'C' and resid 123 through 129
      removed outlier: 3.791A  pdb=" N   ASP C 127 " --> pdb=" O   LEU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 134
    Processing helix  chain 'C' and resid 138 through 151
    Processing helix  chain 'C' and resid 156 through 175
    Processing helix  chain 'C' and resid 179 through 195
    Processing helix  chain 'C' and resid 198 through 203
    Processing helix  chain 'C' and resid 205 through 225
    Processing helix  chain 'C' and resid 229 through 252
    Processing helix  chain 'C' and resid 256 through 269
      removed outlier: 3.687A  pdb=" N   GLU C 265 " --> pdb=" O   VAL C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 273
    Processing helix  chain 'C' and resid 275 through 279
    Processing helix  chain 'C' and resid 283 through 290
    Processing helix  chain 'C' and resid 292 through 305
    Processing helix  chain 'C' and resid 308 through 330
    Processing helix  chain 'C' and resid 337 through 359
    Processing helix  chain 'C' and resid 363 through 381
      removed outlier: 3.837A  pdb=" N   ASN C 379 " --> pdb=" O   GLU C 375 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU C 380 " --> pdb=" O   TYR C 376 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASN C 381 " --> pdb=" O   PHE C 377 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 389
    Processing helix  chain 'C' and resid 392 through 397
    Processing helix  chain 'C' and resid 404 through 422
    Processing helix  chain 'C' and resid 424 through 442
    Processing helix  chain 'C' and resid 447 through 461
    Processing helix  chain 'C' and resid 463 through 495
    Processing helix  chain 'C' and resid 525 through 543
    Processing helix  chain 'C' and resid 595 through 608
    Processing helix  chain 'C' and resid 613 through 621
    Processing helix  chain 'C' and resid 630 through 636
    Processing helix  chain 'C' and resid 684 through 714
    Processing helix  chain 'C' and resid 718 through 731
    Processing helix  chain 'C' and resid 737 through 751
    Processing helix  chain 'K' and resid 32 through 43
    Processing helix  chain 'K' and resid 64 through 69
    Processing helix  chain 'K' and resid 74 through 80
    Processing helix  chain 'K' and resid 97 through 109
    Processing helix  chain 'K' and resid 120 through 130
    Processing helix  chain 'K' and resid 132 through 146
      removed outlier: 3.842A  pdb=" N   ILE K 136 " --> pdb=" O   ILE K 132 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 36 through 46
    Processing helix  chain 'L' and resid 64 through 72
    Processing helix  chain 'L' and resid 103 through 110
    Processing helix  chain 'L' and resid 122 through 130
    Processing helix  chain 'L' and resid 132 through 142
    Processing helix  chain 'R' and resid 53 through 58
    Processing sheet with id=AA1, first strand: chain 'C' and resid 549 through 550
    Processing sheet with id=AA2, first strand: chain 'C' and resid 558 through 559
      removed outlier: 5.597A  pdb=" N   ILE C 591 " --> pdb=" O   VAL C 672 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 610 through 612
    Processing sheet with id=AA4, first strand: chain 'C' and resid 716 through 717
    Processing sheet with id=AA5, first strand: chain 'K' and resid 52 through 54
    Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 54

    464 hydrogen bonds defined for protein.
    1365 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: 2.32

  Time building geometry restraints manager: 3.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.48: 3457
        1.48 -     1.74: 4219
        1.74 -     2.00: 91
        2.00 -     2.26: 0
        2.26 -     2.52: 1
  Bond restraints: 7768
  Sorted by residual:
  bond pdb=" C   GLU L  57 "
       pdb=" N   ARG L  59 "
    ideal  model  delta    sigma   weight residual
    1.329  2.524 -1.195 1.40e-02 5.10e+03 7.29e+03
  bond pdb=" N   ILE C 269 "
       pdb=" CA  ILE C 269 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 9.00e-03 1.23e+04 1.72e+01
  bond pdb=" N   VAL K  56 "
       pdb=" CA  VAL K  56 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.08e-02 8.57e+03 1.29e+01
  bond pdb=" N   ILE C 122 "
       pdb=" CA  ILE C 122 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 1.19e-02 7.06e+03 1.15e+01
  bond pdb=" N   ILE K  48 "
       pdb=" CA  ILE K  48 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.037 1.14e-02 7.69e+03 1.08e+01
  ... (remaining 7763 not shown)

  Histogram of bond angle deviations from ideal:
       88.89 -    99.22: 1
       99.22 -   109.54: 1096
      109.54 -   119.86: 6291
      119.86 -   130.18: 2983
      130.18 -   140.50: 46
  Bond angle restraints: 10417
  Sorted by residual:
  angle pdb=" O   GLU L  57 "
        pdb=" C   GLU L  57 "
        pdb=" N   ARG L  59 "
      ideal   model   delta    sigma   weight residual
     122.59   88.89   33.70 1.33e+00 5.65e-01 6.42e+02
  angle pdb=" C   GLU L  57 "
        pdb=" N   ARG L  59 "
        pdb=" CA  ARG L  59 "
      ideal   model   delta    sigma   weight residual
     121.70  140.50  -18.80 1.80e+00 3.09e-01 1.09e+02
  angle pdb=" C   GLU C 752 "
        pdb=" CA  GLU C 752 "
        pdb=" CB  GLU C 752 "
      ideal   model   delta    sigma   weight residual
     116.54  110.58    5.96 1.15e+00 7.56e-01 2.69e+01
  angle pdb=" CA  VAL L  55 "
        pdb=" C   VAL L  55 "
        pdb=" O   VAL L  55 "
      ideal   model   delta    sigma   weight residual
     122.63  118.27    4.36 8.70e-01 1.32e+00 2.51e+01
  angle pdb=" CA  GLU L  57 "
        pdb=" C   GLU L  57 "
        pdb=" N   ARG L  59 "
      ideal   model   delta    sigma   weight residual
     116.84  125.05   -8.21 1.71e+00 3.42e-01 2.31e+01
  ... (remaining 10412 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.29: 4027
       13.29 -    26.58: 398
       26.58 -    39.87: 200
       39.87 -    53.16: 33
       53.16 -    66.45: 72
  Dihedral angle restraints: 4730
    sinusoidal: 1989
      harmonic: 2741
  Sorted by residual:
  dihedral pdb=" CA  GLU L  57 "
           pdb=" C   GLU L  57 "
           pdb=" N   ARG L  59 "
           pdb=" CA  ARG L  59 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   20.64  -20.64     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ARG C 671 "
           pdb=" CB  ARG C 671 "
           pdb=" CG  ARG C 671 "
           pdb=" CD  ARG C 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.17   58.83     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   VAL K  52 "
           pdb=" CA  VAL K  52 "
           pdb=" CB  VAL K  52 "
           pdb=" CG1 VAL K  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.79   58.21     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 4727 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 337
       0.045 -    0.089: 276
       0.089 -    0.134: 325
       0.134 -    0.179: 195
       0.179 -    0.224: 39
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" CA  ILE C 741 "
            pdb=" N   ILE C 741 "
            pdb=" C   ILE C 741 "
            pdb=" CB  ILE C 741 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE C 183 "
            pdb=" N   ILE C 183 "
            pdb=" C   ILE C 183 "
            pdb=" CB  ILE C 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE C 241 "
            pdb=" N   ILE C 241 "
            pdb=" C   ILE C 241 "
            pdb=" CB  ILE C 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1169 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU L  57 "   -0.155 2.00e-02 2.50e+03   2.13e-01 4.54e+02
        pdb=" C   GLU L  57 "    0.364 2.00e-02 2.50e+03
        pdb=" O   GLU L  57 "   -0.144 2.00e-02 2.50e+03
        pdb=" N   ARG L  59 "   -0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 153 "   -0.279 9.50e-02 1.11e+02   1.25e-01 9.59e+00
        pdb=" NE  ARG C 153 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 153 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 153 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 153 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 180 "    0.273 9.50e-02 1.11e+02   1.22e-01 9.19e+00
        pdb=" NE  ARG C 180 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 180 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 180 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 180 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.90: 3170
        2.90 -     3.40: 8894
        3.40 -     3.90: 14890
        3.90 -     4.40: 16936
        4.40 -     4.90: 24664
  Nonbonded interactions: 68554
  Sorted by model distance:
  nonbonded pdb=" O   LEU K  54 "
            pdb=" OH  TYR K  98 "
     model   vdw
     2.406 2.440
  nonbonded pdb=" O   LEU C 252 "
            pdb=" OG1 THR C 256 "
     model   vdw
     2.416 2.440
  nonbonded pdb=" O   ARG C 642 "
            pdb=" ND2 ASN C 662 "
     model   vdw
     2.456 2.520
  nonbonded pdb=" O   LYS C 457 "
            pdb=" OG1 THR C 460 "
     model   vdw
     2.465 2.440
  nonbonded pdb=" N   GLN C 551 "
            pdb=" O   VAL R  30 "
     model   vdw
     2.468 2.520
  ... (remaining 68549 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
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:             10.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     26.820
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5289
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      :  0.018   1.195   7768  Z= 1.292
  Angle     :  1.410  33.696  10417  Z= 1.135
  Chirality :  0.100   0.224   1172
  Planarity :  0.015   0.213   1323
  Dihedral  : 15.708  66.448   2928
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 21.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 10.74 %
    Favored  : 83.59 %
  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: -1.38 (0.26), residues: 880
  helix: -0.14 (0.19), residues: 600
  sheet: -4.08 (1.35), residues: 10
  loop : -2.44 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R  33 
 HIS   0.007   0.001   HIS C 112 
 PHE   0.015   0.002   PHE C  54 
 TYR   0.019   0.002   TYR C 233 
 ARG   0.005   0.001   ARG K  38 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 147
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7240 (mt)
REVERT: C   83 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7263 (tt0)
REVERT: C  124 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6488 (ptm)
REVERT: C  141 ASN cc_start: 0.5804 (OUTLIER) cc_final: 0.5604 (m-40)
REVERT: C  152 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.6705 (p)
REVERT: C  163 GLN cc_start: 0.6487 (pt0) cc_final: 0.6077 (pt0)
REVERT: C  167 ASP cc_start: 0.6536 (m-30) cc_final: 0.6053 (m-30)
REVERT: C  243 GLU cc_start: 0.6605 (tp30) cc_final: 0.6102 (tp30)
REVERT: C  289 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7344 (mtmt)
REVERT: C  321 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6485 (tt)
REVERT: C  377 PHE cc_start: 0.6537 (p90) cc_final: 0.6151 (p90)
REVERT: C  383 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6217 (ttm170)
REVERT: C  414 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7301 (mtmt)
REVERT: C  416 MET cc_start: 0.7612 (tpt) cc_final: 0.7313 (tpt)
REVERT: C  434 GLN cc_start: 0.6093 (mt0) cc_final: 0.5512 (mt0)
REVERT: C  454 MET cc_start: 0.6804 (tpt) cc_final: 0.6453 (tpp)
REVERT: C  457 LYS cc_start: 0.7370 (tptt) cc_final: 0.7035 (tptt)
REVERT: C  536 ARG cc_start: 0.6673 (ttp-110) cc_final: 0.6344 (ttp-170)
REVERT: C  599 MET cc_start: 0.5267 (mtm) cc_final: 0.4812 (mtm)
REVERT: C  766 TYR cc_start: 0.6493 (t80) cc_final: 0.5954 (t80)
  outliers start: 48
  outliers final: 14
  residues processed: 179
  average time/residue: 0.2475
  time to fit residues: 56.7210
Evaluate side-chains
  158 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0170
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0970
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
C  45 GLN
** C  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 HIS
C 361 ASN
C 675 GLN
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 106 HIS
** L  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  28 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5692
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7768  Z= 0.276
  Angle     :  0.682  12.305  10417  Z= 0.368
  Chirality :  0.044   0.239   1172
  Planarity :  0.006   0.120   1323
  Dihedral  :  4.065  20.390   1000
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 21.90
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.04 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.61 (0.28), residues: 882
  helix:  1.40 (0.20), residues: 603
  sheet: -3.12 (1.01), residues: 21
  loop : -1.69 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C 513 
 HIS   0.008   0.002   HIS K 137 
 PHE   0.028   0.002   PHE C 428 
 TYR   0.030   0.003   TYR C  62 
 ARG   0.011   0.001   ARG C 322 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6926 (ttt) cc_final: 0.6305 (ttt)
REVERT: C   65 VAL cc_start: 0.7328 (t) cc_final: 0.7035 (t)
REVERT: C  130 TYR cc_start: 0.5639 (m-10) cc_final: 0.5417 (m-80)
REVERT: C  152 VAL cc_start: 0.7647 (t) cc_final: 0.7346 (p)
REVERT: C  189 MET cc_start: 0.7254 (ttp) cc_final: 0.6579 (tmm)
REVERT: C  191 MET cc_start: 0.6631 (mmt) cc_final: 0.6127 (mmt)
REVERT: C  203 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6347 (mt-10)
REVERT: C  237 VAL cc_start: 0.6767 (t) cc_final: 0.6393 (t)
REVERT: C  243 GLU cc_start: 0.6948 (tp30) cc_final: 0.6723 (tp30)
REVERT: C  287 MET cc_start: 0.6520 (mtt) cc_final: 0.6303 (mtt)
REVERT: C  289 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7950 (mmmm)
REVERT: C  301 LYS cc_start: 0.6404 (tmmt) cc_final: 0.6161 (ttpp)
REVERT: C  361 ASN cc_start: 0.8084 (t0) cc_final: 0.7873 (t0)
REVERT: C  377 PHE cc_start: 0.7222 (p90) cc_final: 0.6486 (p90)
REVERT: C  454 MET cc_start: 0.6712 (tpt) cc_final: 0.6374 (tpp)
REVERT: C  457 LYS cc_start: 0.7638 (tptt) cc_final: 0.7017 (tptt)
REVERT: C  508 LEU cc_start: 0.7428 (mt) cc_final: 0.7160 (mt)
REVERT: C  589 LYS cc_start: 0.7269 (mmtt) cc_final: 0.6993 (mmmt)
REVERT: C  673 LYS cc_start: 0.7749 (ptmm) cc_final: 0.7389 (ptpp)
REVERT: K  138 PHE cc_start: 0.3932 (m-10) cc_final: 0.3492 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2292
  time to fit residues: 45.7983
Evaluate side-chains
  135 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.1980
   chunk 69 optimal weight:    0.6980
   chunk 56 optimal weight:    0.3980
   chunk 23 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0570
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
** C  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 218 GLN
C 543 HIS
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5790
moved from start:          0.4420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7768  Z= 0.238
  Angle     :  0.615  13.560  10417  Z= 0.335
  Chirality :  0.042   0.320   1172
  Planarity :  0.004   0.047   1323
  Dihedral  :  4.078  20.182   1000
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 18.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.83 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.28), residues: 882
  helix:  1.62 (0.20), residues: 600
  sheet: -2.08 (1.03), residues: 20
  loop : -1.53 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 513 
 HIS   0.006   0.001   HIS C 670 
 PHE   0.026   0.002   PHE C 377 
 TYR   0.028   0.003   TYR K  74 
 ARG   0.006   0.001   ARG C 322 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6915 (ttt) cc_final: 0.6630 (ttt)
REVERT: C  152 VAL cc_start: 0.7724 (t) cc_final: 0.7417 (p)
REVERT: C  183 ILE cc_start: 0.7570 (mt) cc_final: 0.7350 (mt)
REVERT: C  191 MET cc_start: 0.6864 (mmt) cc_final: 0.6264 (mmt)
REVERT: C  198 ARG cc_start: 0.7020 (ptt90) cc_final: 0.6799 (ptt90)
REVERT: C  236 LYS cc_start: 0.6650 (mmpt) cc_final: 0.6403 (mmtt)
REVERT: C  243 GLU cc_start: 0.6688 (tp30) cc_final: 0.6277 (tp30)
REVERT: C  254 LYS cc_start: 0.7171 (mptt) cc_final: 0.6915 (mptt)
REVERT: C  274 LYS cc_start: 0.7800 (pttp) cc_final: 0.6950 (tptp)
REVERT: C  279 MET cc_start: 0.4641 (tmm) cc_final: 0.4212 (tmm)
REVERT: C  289 LYS cc_start: 0.8332 (mmtm) cc_final: 0.7352 (mtmt)
REVERT: C  323 GLU cc_start: 0.7033 (tp30) cc_final: 0.6590 (tp30)
REVERT: C  361 ASN cc_start: 0.8089 (t0) cc_final: 0.7787 (t0)
REVERT: C  377 PHE cc_start: 0.7469 (p90) cc_final: 0.7142 (p90)
REVERT: C  381 ASN cc_start: 0.7606 (t0) cc_final: 0.7219 (t0)
REVERT: C  395 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7031 (mmtm)
REVERT: C  413 ASP cc_start: 0.7408 (m-30) cc_final: 0.7057 (m-30)
REVERT: C  420 ARG cc_start: 0.6469 (ttm110) cc_final: 0.6009 (ttm110)
REVERT: C  457 LYS cc_start: 0.7718 (tptt) cc_final: 0.7334 (tptt)
REVERT: C  589 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7165 (mmmt)
REVERT: C  599 MET cc_start: 0.5485 (mtm) cc_final: 0.4907 (mtm)
REVERT: C  707 ILE cc_start: 0.8091 (mt) cc_final: 0.7851 (mt)
REVERT: K  138 PHE cc_start: 0.4450 (m-10) cc_final: 0.4076 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 148
  average time/residue: 0.2506
  time to fit residues: 47.6256
Evaluate side-chains
  134 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0980
   chunk 56 optimal weight:    0.0980
   chunk 83 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
C 530 HIS
K  88 GLN
K 131 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5899
moved from start:          0.5200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7768  Z= 0.285
  Angle     :  0.656  13.575  10417  Z= 0.356
  Chirality :  0.044   0.306   1172
  Planarity :  0.004   0.058   1323
  Dihedral  :  4.253  19.815   1000
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.78 (0.28), residues: 882
  helix:  1.41 (0.20), residues: 600
  sheet: -1.66 (1.23), residues: 22
  loop : -1.37 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 513 
 HIS   0.008   0.001   HIS C 553 
 PHE   0.024   0.002   PHE C 377 
 TYR   0.027   0.003   TYR C 611 
 ARG   0.007   0.001   ARG C 430 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6853 (ttt) cc_final: 0.6419 (ttt)
REVERT: C  203 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6633 (mt-10)
REVERT: C  237 VAL cc_start: 0.6867 (t) cc_final: 0.6582 (t)
REVERT: C  243 GLU cc_start: 0.6722 (tp30) cc_final: 0.6239 (tp30)
REVERT: C  254 LYS cc_start: 0.7010 (mptt) cc_final: 0.6790 (mptt)
REVERT: C  274 LYS cc_start: 0.7910 (pttp) cc_final: 0.7252 (tptt)
REVERT: C  279 MET cc_start: 0.5294 (tmm) cc_final: 0.4845 (tmm)
REVERT: C  289 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8175 (mmmm)
REVERT: C  323 GLU cc_start: 0.7086 (tp30) cc_final: 0.6663 (tp30)
REVERT: C  361 ASN cc_start: 0.8091 (t0) cc_final: 0.7767 (t0)
REVERT: C  381 ASN cc_start: 0.7884 (t0) cc_final: 0.7610 (t0)
REVERT: C  392 ILE cc_start: 0.8165 (mm) cc_final: 0.7909 (mm)
REVERT: C  413 ASP cc_start: 0.7495 (m-30) cc_final: 0.7150 (m-30)
REVERT: C  426 ASP cc_start: 0.8011 (p0) cc_final: 0.7700 (p0)
REVERT: C  457 LYS cc_start: 0.7775 (tptt) cc_final: 0.7387 (tptt)
REVERT: C  538 PHE cc_start: 0.6972 (t80) cc_final: 0.6682 (t80)
REVERT: C  554 MET cc_start: 0.7291 (mtt) cc_final: 0.7001 (mtt)
REVERT: C  590 HIS cc_start: 0.7353 (m-70) cc_final: 0.6411 (m-70)
REVERT: C  673 LYS cc_start: 0.8109 (ptmm) cc_final: 0.7787 (ptmm)
REVERT: C  707 ILE cc_start: 0.8119 (mt) cc_final: 0.7849 (mt)
REVERT: C  734 PHE cc_start: 0.8184 (p90) cc_final: 0.7775 (p90)
REVERT: C  746 GLU cc_start: 0.7257 (tp30) cc_final: 0.6802 (tp30)
REVERT: K  101 MET cc_start: 0.6734 (mmm) cc_final: 0.5902 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2315
  time to fit residues: 47.4583
Evaluate side-chains
  150 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 79 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** C  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5949
moved from start:          0.5812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   7768  Z= 0.322
  Angle     :  0.674  13.634  10417  Z= 0.367
  Chirality :  0.044   0.300   1172
  Planarity :  0.004   0.060   1323
  Dihedral  :  4.486  19.917   1000
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.39 (0.27), residues: 882
  helix:  1.19 (0.20), residues: 599
  sheet: -1.27 (1.18), residues: 20
  loop : -1.79 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 513 
 HIS   0.009   0.002   HIS C 553 
 PHE   0.023   0.002   PHE C 209 
 TYR   0.024   0.003   TYR C 611 
 ARG   0.008   0.001   ARG C 430 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7825 (mmtm)
REVERT: C   64 MET cc_start: 0.6840 (ttt) cc_final: 0.6448 (ttt)
REVERT: C  203 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6728 (mt-10)
REVERT: C  243 GLU cc_start: 0.6692 (tp30) cc_final: 0.6242 (tp30)
REVERT: C  254 LYS cc_start: 0.6993 (mptt) cc_final: 0.6696 (mptt)
REVERT: C  274 LYS cc_start: 0.7888 (pttp) cc_final: 0.7185 (tptt)
REVERT: C  279 MET cc_start: 0.5544 (tmm) cc_final: 0.5010 (tmm)
REVERT: C  289 LYS cc_start: 0.8477 (mmtm) cc_final: 0.8229 (mmmm)
REVERT: C  323 GLU cc_start: 0.7058 (tp30) cc_final: 0.6591 (tp30)
REVERT: C  361 ASN cc_start: 0.8060 (t0) cc_final: 0.7776 (t0)
REVERT: C  377 PHE cc_start: 0.7585 (p90) cc_final: 0.7308 (p90)
REVERT: C  383 ARG cc_start: 0.7507 (ttp-110) cc_final: 0.7025 (ttp-170)
REVERT: C  413 ASP cc_start: 0.7427 (m-30) cc_final: 0.7149 (m-30)
REVERT: C  457 LYS cc_start: 0.7841 (tptt) cc_final: 0.7367 (tptt)
REVERT: C  536 ARG cc_start: 0.7516 (ttm170) cc_final: 0.7221 (ttp80)
REVERT: C  554 MET cc_start: 0.7304 (mtt) cc_final: 0.7005 (mtt)
REVERT: C  590 HIS cc_start: 0.7263 (m-70) cc_final: 0.6565 (m-70)
REVERT: C  592 LEU cc_start: 0.7040 (mm) cc_final: 0.6548 (mt)
REVERT: C  593 GLN cc_start: 0.6740 (mt0) cc_final: 0.6197 (mt0)
REVERT: C  629 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7058 (tpt-90)
REVERT: C  673 LYS cc_start: 0.8166 (ptmm) cc_final: 0.7633 (ptmm)
REVERT: C  707 ILE cc_start: 0.8147 (mt) cc_final: 0.7881 (mt)
REVERT: K   86 MET cc_start: 0.5446 (mtt) cc_final: 0.5094 (mtt)
REVERT: K  101 MET cc_start: 0.6826 (mmm) cc_final: 0.6029 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2358
  time to fit residues: 48.3524
Evaluate side-chains
  155 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 17 optimal weight:    0.1980
   chunk 52 optimal weight:    0.0050
   chunk 21 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 29 optimal weight:    0.2980
   chunk 46 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5896
moved from start:          0.6035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7768  Z= 0.217
  Angle     :  0.620  13.489  10417  Z= 0.331
  Chirality :  0.042   0.300   1172
  Planarity :  0.004   0.056   1323
  Dihedral  :  4.280  18.498   1000
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.70 (0.28), residues: 882
  helix:  1.47 (0.21), residues: 597
  sheet: -1.39 (1.11), residues: 20
  loop : -1.78 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 109 
 HIS   0.005   0.001   HIS C 553 
 PHE   0.025   0.002   PHE C 216 
 TYR   0.019   0.002   TYR C  74 
 ARG   0.006   0.001   ARG C 430 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7736 (mmtm)
REVERT: C   64 MET cc_start: 0.6642 (ttt) cc_final: 0.6273 (ttt)
REVERT: C  203 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6654 (mt-10)
REVERT: C  237 VAL cc_start: 0.6788 (t) cc_final: 0.6555 (t)
REVERT: C  243 GLU cc_start: 0.6655 (tp30) cc_final: 0.6301 (tp30)
REVERT: C  254 LYS cc_start: 0.7026 (mptt) cc_final: 0.6766 (mptt)
REVERT: C  274 LYS cc_start: 0.7713 (pttp) cc_final: 0.7066 (tptt)
REVERT: C  279 MET cc_start: 0.5464 (tmm) cc_final: 0.4722 (tmm)
REVERT: C  361 ASN cc_start: 0.8017 (t0) cc_final: 0.7750 (t0)
REVERT: C  383 ARG cc_start: 0.7474 (ttp-110) cc_final: 0.6718 (ttp-110)
REVERT: C  405 GLU cc_start: 0.7394 (pp20) cc_final: 0.7082 (tm-30)
REVERT: C  413 ASP cc_start: 0.7391 (m-30) cc_final: 0.7151 (m-30)
REVERT: C  457 LYS cc_start: 0.7800 (tptt) cc_final: 0.7456 (tptt)
REVERT: C  469 LYS cc_start: 0.8339 (mttm) cc_final: 0.8061 (mtpp)
REVERT: C  536 ARG cc_start: 0.7493 (ttm170) cc_final: 0.7186 (ttp80)
REVERT: C  554 MET cc_start: 0.7259 (mtt) cc_final: 0.6960 (mtt)
REVERT: C  592 LEU cc_start: 0.7107 (mm) cc_final: 0.6543 (mt)
REVERT: C  593 GLN cc_start: 0.6830 (mt0) cc_final: 0.6330 (mt0)
REVERT: C  629 ARG cc_start: 0.7648 (mmm160) cc_final: 0.6920 (tpt-90)
REVERT: C  673 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7754 (ptmm)
REVERT: C  707 ILE cc_start: 0.8149 (mt) cc_final: 0.7907 (mt)
REVERT: K   86 MET cc_start: 0.5043 (mtt) cc_final: 0.4767 (mtt)
REVERT: K  101 MET cc_start: 0.6747 (mmm) cc_final: 0.5952 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2475
  time to fit residues: 50.9071
Evaluate side-chains
  156 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 40 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0270
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
C  67 HIS
C 250 HIS
** K  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 137 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5955
moved from start:          0.6441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7768  Z= 0.286
  Angle     :  0.664  13.464  10417  Z= 0.360
  Chirality :  0.044   0.299   1172
  Planarity :  0.004   0.042   1323
  Dihedral  :  4.534  22.852   1000
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.44 (0.27), residues: 882
  helix:  1.25 (0.21), residues: 597
  sheet: -1.45 (1.18), residues: 20
  loop : -1.80 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 513 
 HIS   0.008   0.001   HIS C 553 
 PHE   0.021   0.002   PHE C 209 
 TYR   0.020   0.002   TYR C  62 
 ARG   0.008   0.001   ARG C 322 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6747 (ttt) cc_final: 0.6321 (ttt)
REVERT: C  237 VAL cc_start: 0.6582 (t) cc_final: 0.6313 (t)
REVERT: C  243 GLU cc_start: 0.6636 (tp30) cc_final: 0.6185 (tp30)
REVERT: C  254 LYS cc_start: 0.6936 (mptt) cc_final: 0.6634 (mptt)
REVERT: C  274 LYS cc_start: 0.7773 (pttp) cc_final: 0.7080 (tptt)
REVERT: C  279 MET cc_start: 0.5199 (tmm) cc_final: 0.4891 (tmm)
REVERT: C  323 GLU cc_start: 0.7079 (tp30) cc_final: 0.6594 (tp30)
REVERT: C  361 ASN cc_start: 0.7982 (t0) cc_final: 0.7675 (t0)
REVERT: C  377 PHE cc_start: 0.7607 (p90) cc_final: 0.7311 (p90)
REVERT: C  383 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.6911 (ttm170)
REVERT: C  405 GLU cc_start: 0.7432 (pp20) cc_final: 0.7087 (tm-30)
REVERT: C  413 ASP cc_start: 0.7445 (m-30) cc_final: 0.7154 (m-30)
REVERT: C  457 LYS cc_start: 0.7858 (tptt) cc_final: 0.7556 (tptt)
REVERT: C  469 LYS cc_start: 0.8367 (mttm) cc_final: 0.8161 (mtpp)
REVERT: C  536 ARG cc_start: 0.7514 (ttm170) cc_final: 0.7209 (ttp80)
REVERT: C  554 MET cc_start: 0.7276 (mtt) cc_final: 0.6978 (mtt)
REVERT: C  590 HIS cc_start: 0.7326 (m-70) cc_final: 0.6525 (m-70)
REVERT: C  629 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7032 (tpt-90)
REVERT: C  673 LYS cc_start: 0.8196 (ptmm) cc_final: 0.7990 (ptmm)
REVERT: C  707 ILE cc_start: 0.8186 (mt) cc_final: 0.7935 (mt)
REVERT: K   86 MET cc_start: 0.5198 (mtt) cc_final: 0.4936 (mtt)
REVERT: K  101 MET cc_start: 0.6806 (mmm) cc_final: 0.6004 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2474
  time to fit residues: 51.1495
Evaluate side-chains
  158 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 69 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0370
   chunk 84 optimal weight:    0.2980
   chunk 77 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
K  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5939
moved from start:          0.6670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7768  Z= 0.254
  Angle     :  0.647  13.439  10417  Z= 0.348
  Chirality :  0.043   0.300   1172
  Planarity :  0.004   0.035   1323
  Dihedral  :  4.428  20.840   1000
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.45 (0.27), residues: 882
  helix:  1.30 (0.20), residues: 599
  sheet: -1.99 (1.07), residues: 20
  loop : -1.87 (0.34), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP R  35 
 HIS   0.006   0.001   HIS C 553 
 PHE   0.019   0.002   PHE C  54 
 TYR   0.022   0.002   TYR K  74 
 ARG   0.007   0.001   ARG C 322 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6813 (tp30)
REVERT: C   44 ILE cc_start: 0.8432 (mt) cc_final: 0.8201 (mt)
REVERT: C   47 LYS cc_start: 0.8027 (mptt) cc_final: 0.7526 (mptt)
REVERT: C   64 MET cc_start: 0.6719 (ttt) cc_final: 0.6294 (ttt)
REVERT: C  254 LYS cc_start: 0.6918 (mptt) cc_final: 0.6689 (mptt)
REVERT: C  274 LYS cc_start: 0.7747 (pttp) cc_final: 0.7090 (tptt)
REVERT: C  279 MET cc_start: 0.5324 (tmm) cc_final: 0.4889 (tmm)
REVERT: C  323 GLU cc_start: 0.7032 (tp30) cc_final: 0.6556 (tp30)
REVERT: C  361 ASN cc_start: 0.7926 (t0) cc_final: 0.7645 (t0)
REVERT: C  377 PHE cc_start: 0.7617 (p90) cc_final: 0.7395 (p90)
REVERT: C  405 GLU cc_start: 0.7427 (pp20) cc_final: 0.7067 (tm-30)
REVERT: C  413 ASP cc_start: 0.7445 (m-30) cc_final: 0.7207 (m-30)
REVERT: C  457 LYS cc_start: 0.7870 (tptt) cc_final: 0.7581 (tptt)
REVERT: C  469 LYS cc_start: 0.8364 (mttm) cc_final: 0.8138 (mtpp)
REVERT: C  536 ARG cc_start: 0.7506 (ttm170) cc_final: 0.7147 (ttp80)
REVERT: C  589 LYS cc_start: 0.7792 (mppt) cc_final: 0.7552 (mppt)
REVERT: C  593 GLN cc_start: 0.6826 (mt0) cc_final: 0.6250 (mt0)
REVERT: C  599 MET cc_start: 0.5675 (mtm) cc_final: 0.4883 (mtm)
REVERT: C  629 ARG cc_start: 0.7721 (mmm160) cc_final: 0.6972 (tpt-90)
REVERT: C  673 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7885 (ptmm)
REVERT: C  707 ILE cc_start: 0.8174 (mt) cc_final: 0.7933 (mt)
REVERT: C  734 PHE cc_start: 0.8249 (p90) cc_final: 0.8024 (p90)
REVERT: K  101 MET cc_start: 0.6750 (mmm) cc_final: 0.5953 (mmm)
REVERT: K  105 LEU cc_start: 0.6994 (mt) cc_final: 0.6729 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2573
  time to fit residues: 53.3075
Evaluate side-chains
  153 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 49 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0980
   chunk 64 optimal weight:    0.6980
   chunk 25 optimal weight:    0.1980
   chunk 74 optimal weight:    0.9990
   chunk 78 optimal weight:    0.1980
   chunk 82 optimal weight:    0.8980
   chunk 54 optimal weight:    0.2980
   chunk 87 optimal weight:    2.9990
   chunk 53 optimal weight:    0.1980
   overall best weight:    0.1980

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

Flipped N/Q/H residues before XYZ refinement:
** K  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5863
moved from start:          0.6796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7768  Z= 0.183
  Angle     :  0.616  13.425  10417  Z= 0.324
  Chirality :  0.041   0.302   1172
  Planarity :  0.003   0.033   1323
  Dihedral  :  4.232  20.526   1000
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.85 (0.28), residues: 882
  helix:  1.65 (0.21), residues: 594
  sheet: -1.55 (1.15), residues: 20
  loop : -1.80 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R  35 
 HIS   0.004   0.001   HIS C 530 
 PHE   0.022   0.002   PHE C 209 
 TYR   0.019   0.002   TYR K  74 
 ARG   0.005   0.001   ARG C 247 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 ILE cc_start: 0.8295 (mt) cc_final: 0.8092 (mt)
REVERT: C   47 LYS cc_start: 0.7970 (mptt) cc_final: 0.7515 (mptt)
REVERT: C   64 MET cc_start: 0.6546 (ttt) cc_final: 0.6186 (ttt)
REVERT: C  163 GLN cc_start: 0.6791 (pt0) cc_final: 0.6509 (pt0)
REVERT: C  171 ARG cc_start: 0.5731 (mtm-85) cc_final: 0.5508 (mtm-85)
REVERT: C  191 MET cc_start: 0.6772 (mmt) cc_final: 0.6566 (mmt)
REVERT: C  206 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6114 (tm-30)
REVERT: C  211 GLU cc_start: 0.7097 (pp20) cc_final: 0.6590 (pt0)
REVERT: C  212 MET cc_start: 0.5926 (tmm) cc_final: 0.5583 (ppp)
REVERT: C  243 GLU cc_start: 0.6636 (tp30) cc_final: 0.6272 (tp30)
REVERT: C  254 LYS cc_start: 0.6901 (mptt) cc_final: 0.6604 (mptt)
REVERT: C  274 LYS cc_start: 0.7520 (pttp) cc_final: 0.6937 (tptt)
REVERT: C  279 MET cc_start: 0.5146 (tmm) cc_final: 0.4788 (tmm)
REVERT: C  323 GLU cc_start: 0.6971 (tp30) cc_final: 0.6661 (tp30)
REVERT: C  361 ASN cc_start: 0.7924 (t0) cc_final: 0.7660 (t0)
REVERT: C  405 GLU cc_start: 0.7378 (pp20) cc_final: 0.7018 (tm-30)
REVERT: C  413 ASP cc_start: 0.7457 (m-30) cc_final: 0.7252 (m-30)
REVERT: C  457 LYS cc_start: 0.7783 (tptt) cc_final: 0.7536 (tptt)
REVERT: C  469 LYS cc_start: 0.8296 (mttm) cc_final: 0.8050 (mtpp)
REVERT: C  524 ILE cc_start: 0.7784 (mm) cc_final: 0.7503 (mm)
REVERT: C  536 ARG cc_start: 0.7383 (ttm170) cc_final: 0.7110 (ttp80)
REVERT: C  554 MET cc_start: 0.7281 (mtt) cc_final: 0.7047 (mtt)
REVERT: C  589 LYS cc_start: 0.7691 (mppt) cc_final: 0.7448 (mppt)
REVERT: C  599 MET cc_start: 0.5475 (mtm) cc_final: 0.4673 (mtm)
REVERT: C  673 LYS cc_start: 0.7924 (ptmm) cc_final: 0.7553 (ptmm)
REVERT: C  700 LYS cc_start: 0.6498 (ptmm) cc_final: 0.6150 (ptmm)
REVERT: C  707 ILE cc_start: 0.8103 (mt) cc_final: 0.7893 (mt)
REVERT: K  101 MET cc_start: 0.6704 (mmm) cc_final: 0.5842 (mmm)
REVERT: K  105 LEU cc_start: 0.7089 (mt) cc_final: 0.6786 (pp)
REVERT: K  130 LEU cc_start: 0.6563 (tp) cc_final: 0.6345 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2492
  time to fit residues: 52.1143
Evaluate side-chains
  154 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    0.1980
   chunk 60 optimal weight:    0.7980
   chunk 91 optimal weight:    0.1980
   chunk 84 optimal weight:    0.0050
   chunk 72 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0170
   chunk 77 optimal weight:    0.0370
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.0910

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

Flipped N/Q/H residues before XYZ refinement:
C 593 GLN
C 641 GLN
K  88 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5796
moved from start:          0.6888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7768  Z= 0.157
  Angle     :  0.594  13.396  10417  Z= 0.311
  Chirality :  0.040   0.302   1172
  Planarity :  0.003   0.033   1323
  Dihedral  :  4.065  20.827   1000
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.16 (0.28), residues: 882
  helix:  1.89 (0.21), residues: 595
  sheet: -1.51 (1.16), residues: 20
  loop : -1.71 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R  35 
 HIS   0.004   0.001   HIS L  60 
 PHE   0.037   0.002   PHE C 216 
 TYR   0.021   0.002   TYR C 201 
 ARG   0.005   0.000   ARG C 430 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6416 (ttt) cc_final: 0.6100 (ttt)
REVERT: C  206 GLU cc_start: 0.6352 (tm-30) cc_final: 0.5901 (tm-30)
REVERT: C  211 GLU cc_start: 0.7056 (pp20) cc_final: 0.6486 (pt0)
REVERT: C  212 MET cc_start: 0.6108 (tmm) cc_final: 0.5763 (tmm)
REVERT: C  243 GLU cc_start: 0.6516 (tp30) cc_final: 0.6187 (tp30)
REVERT: C  272 HIS cc_start: 0.7007 (m90) cc_final: 0.6632 (m-70)
REVERT: C  274 LYS cc_start: 0.7314 (pttp) cc_final: 0.6774 (tptt)
REVERT: C  279 MET cc_start: 0.4871 (tmm) cc_final: 0.4538 (tmm)
REVERT: C  323 GLU cc_start: 0.6931 (tp30) cc_final: 0.6391 (tp30)
REVERT: C  361 ASN cc_start: 0.7584 (t0) cc_final: 0.7327 (t0)
REVERT: C  377 PHE cc_start: 0.7571 (p90) cc_final: 0.7204 (p90)
REVERT: C  405 GLU cc_start: 0.7336 (pp20) cc_final: 0.6972 (tm-30)
REVERT: C  413 ASP cc_start: 0.7467 (m-30) cc_final: 0.7252 (m-30)
REVERT: C  457 LYS cc_start: 0.7830 (tptt) cc_final: 0.7586 (tptt)
REVERT: C  469 LYS cc_start: 0.8241 (mttm) cc_final: 0.7999 (mtpp)
REVERT: C  524 ILE cc_start: 0.7657 (mm) cc_final: 0.7441 (mm)
REVERT: C  536 ARG cc_start: 0.7339 (ttm170) cc_final: 0.7126 (ttm170)
REVERT: C  554 MET cc_start: 0.7107 (mtt) cc_final: 0.6900 (mtt)
REVERT: C  589 LYS cc_start: 0.7603 (mppt) cc_final: 0.7363 (mppt)
REVERT: C  593 GLN cc_start: 0.7392 (tm130) cc_final: 0.7127 (tm130)
REVERT: C  599 MET cc_start: 0.5366 (mtm) cc_final: 0.4632 (mtm)
REVERT: C  700 LYS cc_start: 0.6638 (ptmm) cc_final: 0.6310 (ptmm)
REVERT: C  707 ILE cc_start: 0.8070 (mt) cc_final: 0.7868 (mt)
REVERT: C  746 GLU cc_start: 0.7163 (tp30) cc_final: 0.6786 (tp30)
REVERT: K  101 MET cc_start: 0.6590 (mmm) cc_final: 0.5655 (mmm)
REVERT: K  119 ASN cc_start: 0.6616 (t0) cc_final: 0.6340 (p0)
REVERT: K  130 LEU cc_start: 0.6409 (tp) cc_final: 0.6201 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2428
  time to fit residues: 48.3040
Evaluate side-chains
  149 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 20 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 75 optimal weight:    0.3980
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 64 optimal weight:    0.4980
   chunk 4 optimal weight:    0.1980
   chunk 52 optimal weight:    0.1980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
C 593 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.207088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.181902 restraints weight = 13118.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.185885 restraints weight = 8276.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.188697 restraints weight = 5661.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5878
moved from start:          0.7069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7768  Z= 0.227
  Angle     :  0.630  13.359  10417  Z= 0.335
  Chirality :  0.041   0.299   1172
  Planarity :  0.004   0.054   1323
  Dihedral  :  4.263  20.931   1000
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.28), residues: 882
  helix:  1.77 (0.21), residues: 593
  sheet: -1.56 (1.19), residues: 20
  loop : -1.76 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R  35 
 HIS   0.005   0.001   HIS C 553 
 PHE   0.020   0.002   PHE C 209 
 TYR   0.017   0.002   TYR K  74 
 ARG   0.007   0.000   ARG C 430 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2312.21 seconds
wall clock time: 42 minutes 3.20 seconds (2523.20 seconds total)