Starting phenix.real_space_refine
on Wed Aug  7 20:36:13 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/08_2024/6mec_9106.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/08_2024/6mec_9106.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/08_2024/6mec_9106.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/08_2024/6mec_9106.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/08_2024/6mec_9106.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/08_2024/6mec_9106.cif"
  }
  resolution = 3.6
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     P     832      5.49       5
     Mg     51      5.21       5
     S       8      5.16       5
     Na      1      4.78       5
     C   10129      2.51       5
     N    3918      2.21       5
     O    6337      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C ARG  413": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 21276
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 17537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 818, 17537
          Classifications: {'DNA': 1, 'RNA': 817}
          Modifications used: {'rna2p_pur': 53, 'rna2p_pyr': 34, 'rna3p_pur': 407, 'rna3p_pyr': 323}
          Link IDs: {'rna2p': 87, 'rna3p': 730}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 294
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "C"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3393
          Classifications: {'peptide': 414}
          Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 398}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 51
          Unusual residues: {' MG': 50, ' NA': 1}
          Classifications: {'undetermined': 51}
          Link IDs: {None: 50}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 13.70, per 1000 atoms: 0.64
  Number of scatterers: 21276
  At special positions: 0
  Unit cell: (116.13, 154.05, 237, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S       8     16.00
     P     832     15.00
     Mg     51     11.99
     Na      1     11.00
     O    6337      8.00
     N    3918      7.00
     C   10129      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: 13.15
  Conformation dependent library (CDL) restraints added in 826.1 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 3 sheets defined
      53.4% alpha, 6.3% beta
      279 base pairs and 440 stacking pairs defined.
    Time for finding SS restraints: 11.69
  Creating SS restraints...
    Processing helix  chain 'C' and resid 27 through 48
      removed outlier: 4.384A  pdb=" N   ASN C  32 " --> pdb=" O   TRP C  28 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   ARG C  33 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL C  35 " --> pdb=" O   ALA C  31 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU C  48 " --> pdb=" O   LYS C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 63
    Processing helix  chain 'C' and resid 64 through 77
    Processing helix  chain 'C' and resid 93 through 105
      removed outlier: 4.176A  pdb=" N   LEU C 104 " --> pdb=" O   ALA C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 154
      Proline residue:  C 149  - end of helix
      removed outlier: 3.567A  pdb=" N   THR C 153 " --> pdb=" O   PRO C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 179
      removed outlier: 3.535A  pdb=" N   ALA C 172 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 212 through 222
    Processing helix  chain 'C' and resid 243 through 252
      removed outlier: 3.752A  pdb=" N   LEU C 252 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 259
    Processing helix  chain 'C' and resid 285 through 300
      removed outlier: 3.520A  pdb=" N   GLU C 300 " --> pdb=" O   GLU C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 356
    Processing helix  chain 'C' and resid 360 through 378
      Proline residue:  C 370  - end of helix
    Processing helix  chain 'C' and resid 384 through 406
    Processing helix  chain 'C' and resid 411 through 420
    Processing helix  chain 'C' and resid 448 through 452
      removed outlier: 3.837A  pdb=" N   THR C 452 " --> pdb=" O   ALA C 449 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119
      removed outlier: 3.994A  pdb=" N   VAL C 117 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 273
      removed outlier: 4.190A  pdb=" N   PHE C 277 " --> pdb=" O   ALA C 191 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA C 191 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321

    163 hydrogen bonds defined for protein.
    465 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      725 hydrogen bonds
      1260 hydrogen bond angles
      0 basepair planarities
      279 basepair parallelities
      440 stacking parallelities
  Total time for adding SS restraints: 15.64

  Time building geometry restraints manager: 14.05 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2006
        1.32 -     1.44: 11160
        1.44 -     1.56: 8588
        1.56 -     1.68: 1663
        1.68 -     1.80: 12
  Bond restraints: 23429
  Sorted by residual:
  bond pdb=" N   PRO C 132 "
       pdb=" CD  PRO C 132 "
    ideal  model  delta    sigma   weight residual
    1.473  1.416  0.057 1.40e-02 5.10e+03 1.64e+01
  bond pdb=" N   PRO C 245 "
       pdb=" CD  PRO C 245 "
    ideal  model  delta    sigma   weight residual
    1.473  1.430  0.043 1.40e-02 5.10e+03 9.60e+00
  bond pdb=" CB  ASN C 389 "
       pdb=" CG  ASN C 389 "
    ideal  model  delta    sigma   weight residual
    1.516  1.446  0.070 2.50e-02 1.60e+03 7.74e+00
  bond pdb=" CB  ARG C 406 "
       pdb=" CG  ARG C 406 "
    ideal  model  delta    sigma   weight residual
    1.520  1.438  0.082 3.00e-02 1.11e+03 7.49e+00
  bond pdb=" CE3 TRP C 402 "
       pdb=" CZ3 TRP C 402 "
    ideal  model  delta    sigma   weight residual
    1.382  1.303  0.079 3.00e-02 1.11e+03 6.89e+00
  ... (remaining 23424 not shown)

  Histogram of bond angle deviations from ideal:
       94.17 -   102.87: 1653
      102.87 -   111.56: 14206
      111.56 -   120.26: 11824
      120.26 -   128.95: 7268
      128.95 -   137.65: 841
  Bond angle restraints: 35792
  Sorted by residual:
  angle pdb=" C3'   A A 481 "
        pdb=" O3'   A A 481 "
        pdb=" P     U A 482 "
      ideal   model   delta    sigma   weight residual
     120.20  128.24   -8.04 1.50e+00 4.44e-01 2.87e+01
  angle pdb=" C3'   U A 545 "
        pdb=" O3'   U A 545 "
        pdb=" P     C A 546 "
      ideal   model   delta    sigma   weight residual
     120.20  127.78   -7.58 1.50e+00 4.44e-01 2.55e+01
  angle pdb=" C3'   A A 462 "
        pdb=" O3'   A A 462 "
        pdb=" P     U A 463 "
      ideal   model   delta    sigma   weight residual
     120.20  127.58   -7.38 1.50e+00 4.44e-01 2.42e+01
  angle pdb=" O3'   A A  12 "
        pdb=" C3'   A A  12 "
        pdb=" C2'   A A  12 "
      ideal   model   delta    sigma   weight residual
     113.70  120.85   -7.15 1.50e+00 4.44e-01 2.27e+01
  angle pdb=" C3'   C A 666 "
        pdb=" O3'   C A 666 "
        pdb=" P     A A 667 "
      ideal   model   delta    sigma   weight residual
     120.20  127.31   -7.11 1.50e+00 4.44e-01 2.24e+01
  ... (remaining 35787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 12656
       35.58 -    71.16: 2052
       71.16 -   106.74: 274
      106.74 -   142.33: 8
      142.33 -   177.91: 10
  Dihedral angle restraints: 15000
    sinusoidal: 13802
      harmonic: 1198
  Sorted by residual:
  dihedral pdb=" O4'   U A 258 "
           pdb=" C1'   U A 258 "
           pdb=" N1    U A 258 "
           pdb=" C2    U A 258 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.91 -177.91     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U A 839 "
           pdb=" C1'   U A 839 "
           pdb=" N1    U A 839 "
           pdb=" C2    U A 839 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   45.05 -173.05     1      1.70e+01 3.46e-03 6.62e+01
  dihedral pdb=" CA  TYR C 273 "
           pdb=" C   TYR C 273 "
           pdb=" N   ALA C 274 "
           pdb=" CA  ALA C 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.17  -39.83     0      5.00e+00 4.00e-02 6.35e+01
  ... (remaining 14997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 4117
       0.088 -    0.175: 475
       0.175 -    0.263: 40
       0.263 -    0.351: 8
       0.351 -    0.439: 4
  Chirality restraints: 4644
  Sorted by residual:
  chirality pdb=" C1'   A A 401 "
            pdb=" O4'   A A 401 "
            pdb=" C2'   A A 401 "
            pdb=" N9    A A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.00    0.44 2.00e-01 2.50e+01 4.81e+00
  chirality pdb=" C3'   G A   8 "
            pdb=" C4'   G A   8 "
            pdb=" O3'   G A   8 "
            pdb=" C2'   G A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.10   -0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" C3'   G A 832 "
            pdb=" C4'   G A 832 "
            pdb=" O3'   G A 832 "
            pdb=" C2'   G A 832 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.11   -0.37 2.00e-01 2.50e+01 3.40e+00
  ... (remaining 4641 not shown)

  Planarity restraints: 1417
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 238 "   -0.049 2.00e-02 2.50e+03   2.15e-02 1.27e+01
        pdb=" N9    A A 238 "    0.047 2.00e-02 2.50e+03
        pdb=" C8    A A 238 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    A A 238 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A A 238 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    A A 238 "   -0.008 2.00e-02 2.50e+03
        pdb=" N6    A A 238 "   -0.013 2.00e-02 2.50e+03
        pdb=" N1    A A 238 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A A 238 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    A A 238 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A A 238 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 407 "    0.057 5.00e-02 4.00e+02   8.68e-02 1.20e+01
        pdb=" N   PRO C 408 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO C 408 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C 408 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 401 "    0.044 2.00e-02 2.50e+03   1.84e-02 9.34e+00
        pdb=" N9    A A 401 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8    A A 401 "   -0.007 2.00e-02 2.50e+03
        pdb=" N7    A A 401 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    A A 401 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A A 401 "    0.010 2.00e-02 2.50e+03
        pdb=" N6    A A 401 "    0.011 2.00e-02 2.50e+03
        pdb=" N1    A A 401 "    0.008 2.00e-02 2.50e+03
        pdb=" C2    A A 401 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    A A 401 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A A 401 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1414 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 75
        2.31 -     2.96: 9335
        2.96 -     3.60: 36914
        3.60 -     4.25: 64238
        4.25 -     4.90: 82886
  Nonbonded interactions: 193448
  Sorted by model distance:
  nonbonded pdb=" CZ2 TRP C  28 "
            pdb=" CD  LYS C  73 "
     model   vdw
     1.659 3.740
  nonbonded pdb=" NE  ARG C 380 "
            pdb=" OE1 GLN C 455 "
     model   vdw
     1.667 3.120
  nonbonded pdb=" P     U A   1 "
            pdb=" O2'   A A 860 "
     model   vdw
     1.676 3.400
  nonbonded pdb=" O   LEU C 356 "
            pdb=" CH2 TRP C 402 "
     model   vdw
     1.793 3.340
  nonbonded pdb=" O2'   A A 428 "
            pdb=" OP1   A A 429 "
     model   vdw
     1.851 3.040
  ... (remaining 193443 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             19.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         3.100
  Set scattering table:                    0.000
  Process input model:                     76.870
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  102.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
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      :  0.010   0.099  23429  Z= 0.612
  Angle     :  1.213  12.467  35792  Z= 0.589
  Chirality :  0.058   0.439   4644
  Planarity :  0.008   0.087   1417
  Dihedral  : 25.555 177.907  14224
  Min Nonbonded Distance : 1.659

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.73 %
    Favored  : 86.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.50 %

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: -4.93 (0.32), residues: 408
  helix: -3.26 (0.23), residues: 212
  sheet: -1.60 (0.94), residues: 34
  loop : -3.49 (0.42), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.006   TRP C 324 
 HIS   0.018   0.006   HIS C 346 
 PHE   0.051   0.006   PHE C 231 
 TYR   0.035   0.004   TYR C 378 
 ARG   0.009   0.002   ARG C 163 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: C  231 PHE cc_start: 0.8259 (p90) cc_final: 0.7870 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.4976
  time to fit residues: 73.0442
Evaluate side-chains
  48 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
C  32 ASN
C 202 HIS
C 269 ASN
C 341 ASN
C 346 HIS
** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 407 HIS
C 417 ASN
C 455 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  23429  Z= 0.238
  Angle     :  0.716   8.889  35792  Z= 0.360
  Chirality :  0.037   0.274   4644
  Planarity :  0.006   0.051   1417
  Dihedral  : 25.968 179.698  13361
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 10.14 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -3.24 (0.38), residues: 408
  helix: -1.47 (0.32), residues: 216
  sheet: -1.58 (0.84), residues: 34
  loop : -3.17 (0.45), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.004   TRP C 396 
 HIS   0.008   0.002   HIS C 346 
 PHE   0.031   0.003   PHE C 231 
 TYR   0.020   0.003   TYR C  66 
 ARG   0.008   0.001   ARG C 357 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.991 
Fit side-chains
  outliers start: 10
  outliers final: 7
  residues processed: 70
  average time/residue: 0.4411
  time to fit residues: 44.1318
Evaluate side-chains
  59 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   65 PHE
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  417 ASN
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9980
   chunk 120 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
C 341 ASN
** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  23429  Z= 0.165
  Angle     :  0.628   8.032  35792  Z= 0.315
  Chirality :  0.032   0.265   4644
  Planarity :  0.005   0.046   1417
  Dihedral  : 25.676 178.047  13361
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 13.24 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -2.15 (0.41), residues: 408
  helix: -0.36 (0.34), residues: 217
  sheet: -1.26 (0.79), residues: 34
  loop : -3.01 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP C 396 
 HIS   0.004   0.001   HIS C 397 
 PHE   0.020   0.002   PHE C 231 
 TYR   0.010   0.002   TYR C 109 
 ARG   0.009   0.001   ARG C 413 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.232 
Fit side-chains
REVERT: C  405 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8315 (ttt-90)
  outliers start: 13
  outliers final: 5
  residues processed: 73
  average time/residue: 0.4576
  time to fit residues: 48.2286
Evaluate side-chains
  55 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  405 ARG
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0020
   chunk 118 optimal weight:    0.5980
   chunk 106 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.8592

-------------------------------------------------------------------------------
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: 0.7704
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  23429  Z= 0.237
  Angle     :  0.662   8.901  35792  Z= 0.331
  Chirality :  0.034   0.269   4644
  Planarity :  0.005   0.039   1417
  Dihedral  : 25.648 179.756  13361
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 14.65 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.88 (0.42), residues: 408
  helix: -0.07 (0.35), residues: 214
  sheet: -0.78 (0.85), residues: 32
  loop : -3.04 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 402 
 HIS   0.007   0.002   HIS C 346 
 PHE   0.016   0.002   PHE C 231 
 TYR   0.019   0.002   TYR C 109 
 ARG   0.006   0.001   ARG C  33 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 1.032 
Fit side-chains
REVERT: C  246 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7696 (mtt)
REVERT: C  379 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8534 (p-80)
  outliers start: 15
  outliers final: 6
  residues processed: 58
  average time/residue: 0.3614
  time to fit residues: 31.9202
Evaluate side-chains
  54 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 88 optimal weight:    0.1980
   chunk 49 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 60 optimal weight:   20.0000
   chunk 106 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    2.2184

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

Flipped N/Q/H residues before XYZ refinement:
C 140 GLN
C 266 GLN
C 269 ASN
C 346 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  23429  Z= 0.270
  Angle     :  0.680   9.026  35792  Z= 0.340
  Chirality :  0.034   0.270   4644
  Planarity :  0.005   0.044   1417
  Dihedral  : 25.646 178.847  13361
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 15.49 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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: -1.71 (0.42), residues: 408
  helix:  0.07 (0.35), residues: 214
  sheet: -0.71 (0.89), residues: 30
  loop : -2.91 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 402 
 HIS   0.008   0.002   HIS C 346 
 PHE   0.025   0.002   PHE C 231 
 TYR   0.015   0.002   TYR C 109 
 ARG   0.005   0.001   ARG C 327 

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 1.072 
Fit side-chains
REVERT: C   70 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8108 (mm)
REVERT: C  246 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7662 (mtt)
  outliers start: 17
  outliers final: 10
  residues processed: 60
  average time/residue: 0.3751
  time to fit residues: 34.5566
Evaluate side-chains
  55 residues out of total 355 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  299 LYS
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   chunk 69 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 119 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9980
   overall best weight:    2.7384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: