Starting phenix.real_space_refine
on Sat Aug  3 12:40:52 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/08_2024/8kgl_37225.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/08_2024/8kgl_37225.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/08_2024/8kgl_37225.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/08_2024/8kgl_37225.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/08_2024/8kgl_37225.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/08_2024/8kgl_37225.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      24      5.16       5
     C    5210      2.51       5
     N    1386      2.21       5
     O    1464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  744": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  785": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  710": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  744": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  785": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  923": "CD1" <-> "CD2" "CE1" <-> "CE2"
  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: 8084
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 4042
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 468}
    Chain: "B"
      Number of atoms: 4042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 4042
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 468}
  Time building chain proxies: 5.71, per 1000 atoms: 0.71
  Number of scatterers: 8084
  At special positions: 0
  Unit cell: (150.15, 79.95, 108.55, 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      24     16.00
     O    1464      8.00
     N    1386      7.00
     C    5210      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: 3.00
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 10 sheets defined
      51.3% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 701 through 707
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 737 through 749
    Processing helix  chain 'A' and resid 754 through 765
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 4.926A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 820
      removed outlier: 3.620A  pdb=" N   TRP A 820 " --> pdb=" O   GLU A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 830
      removed outlier: 4.176A  pdb=" N   GLY A 829 " --> pdb=" O   PHE A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 846
      removed outlier: 3.709A  pdb=" N   ILE A 845 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 877
    Processing helix  chain 'A' and resid 882 through 893
    Processing helix  chain 'A' and resid 942 through 951
    Processing helix  chain 'A' and resid 981 through 990
      removed outlier: 3.741A  pdb=" N   ARG A 985 " --> pdb=" O   ASN A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1003
    Processing helix  chain 'A' and resid 1027 through 1070
      removed outlier: 3.639A  pdb=" N   ILE A1031 " --> pdb=" O   THR A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
    Processing helix  chain 'A' and resid 1070 through 1075
    Processing helix  chain 'A' and resid 1081 through 1092
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1116
    Processing helix  chain 'A' and resid 1122 through 1126
    Processing helix  chain 'A' and resid 1134 through 1159
      removed outlier: 3.664A  pdb=" N   LYS A1138 " --> pdb=" O   LEU A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1186
    Processing helix  chain 'B' and resid 702 through 707
    Processing helix  chain 'B' and resid 715 through 729
    Processing helix  chain 'B' and resid 737 through 749
    Processing helix  chain 'B' and resid 754 through 766
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 4.990A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 820
      removed outlier: 3.637A  pdb=" N   TRP B 820 " --> pdb=" O   GLU B 817 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 846
      removed outlier: 3.725A  pdb=" N   ILE B 845 " --> pdb=" O   PRO B 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 877
    Processing helix  chain 'B' and resid 882 through 893
    Processing helix  chain 'B' and resid 942 through 951
    Processing helix  chain 'B' and resid 981 through 990
      removed outlier: 3.845A  pdb=" N   ARG B 985 " --> pdb=" O   ASN B 981 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1027 through 1070
      removed outlier: 3.684A  pdb=" N   ILE B1031 " --> pdb=" O   THR B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1070 through 1075
    Processing helix  chain 'B' and resid 1081 through 1092
      removed outlier: 3.523A  pdb=" N   ALA B1085 " --> pdb=" O   ASP B1081 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS B1092 " --> pdb=" O   ILE B1088 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1098 through 1104
      removed outlier: 3.522A  pdb=" N   ILE B1102 " --> pdb=" O   ASN B1098 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1116
    Processing helix  chain 'B' and resid 1122 through 1126
    Processing helix  chain 'B' and resid 1130 through 1133
      removed outlier: 3.538A  pdb=" N   LEU B1133 " --> pdb=" O   ALA B1130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1130 through 1133'
    Processing helix  chain 'B' and resid 1134 through 1159
      removed outlier: 4.051A  pdb=" N   LYS B1138 " --> pdb=" O   LEU B1134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 779 through 782
    Processing sheet with id=AA2, first strand: chain 'A' and resid 849 through 851
    Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913
    Processing sheet with id=AA4, first strand: chain 'A' and resid 923 through 926
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1014 through 1016
    Processing sheet with id=AA6, first strand: chain 'B' and resid 779 through 782
    Processing sheet with id=AA7, first strand: chain 'B' and resid 849 through 851
    Processing sheet with id=AA8, first strand: chain 'B' and resid 909 through 913
    Processing sheet with id=AA9, first strand: chain 'B' and resid 923 through 926
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1014 through 1016

    382 hydrogen bonds defined for protein.
    1077 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: 2.25

  Time building geometry restraints manager: 3.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2396
        1.34 -     1.45: 1439
        1.45 -     1.57: 4409
        1.57 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 8286
  Sorted by residual:
  bond pdb=" C   TYR A 776 "
       pdb=" N   PRO A 777 "
    ideal  model  delta    sigma   weight residual
    1.332  1.310  0.022 1.12e-02 7.97e+03 3.71e+00
  bond pdb=" N   ARG B1131 "
       pdb=" CA  ARG B1131 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.024 1.35e-02 5.49e+03 3.23e+00
  bond pdb=" CA  GLN A1129 "
       pdb=" C   GLN A1129 "
    ideal  model  delta    sigma   weight residual
    1.523  1.547 -0.023 1.34e-02 5.57e+03 3.05e+00
  bond pdb=" CB  TRP A1170 "
       pdb=" CG  TRP A1170 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.93e+00
  bond pdb=" CB  TRP B1170 "
       pdb=" CG  TRP B1170 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.93e+00
  ... (remaining 8281 not shown)

  Histogram of bond angle deviations from ideal:
       97.97 -   105.18: 164
      105.18 -   112.38: 4119
      112.38 -   119.59: 2793
      119.59 -   126.80: 4029
      126.80 -   134.01: 99
  Bond angle restraints: 11204
  Sorted by residual:
  angle pdb=" N   SER B1127 "
        pdb=" CA  SER B1127 "
        pdb=" C   SER B1127 "
      ideal   model   delta    sigma   weight residual
     112.34  122.94  -10.60 1.30e+00 5.92e-01 6.65e+01
  angle pdb=" N   SER A1127 "
        pdb=" CA  SER A1127 "
        pdb=" C   SER A1127 "
      ideal   model   delta    sigma   weight residual
     110.80  123.32  -12.52 2.13e+00 2.20e-01 3.45e+01
  angle pdb=" N   GLY A 786 "
        pdb=" CA  GLY A 786 "
        pdb=" C   GLY A 786 "
      ideal   model   delta    sigma   weight residual
     110.56  116.02   -5.46 1.36e+00 5.41e-01 1.61e+01
  angle pdb=" N   ARG B1131 "
        pdb=" CA  ARG B1131 "
        pdb=" C   ARG B1131 "
      ideal   model   delta    sigma   weight residual
     112.87  117.52   -4.65 1.20e+00 6.94e-01 1.50e+01
  angle pdb=" N   ASN B 851 "
        pdb=" CA  ASN B 851 "
        pdb=" C   ASN B 851 "
      ideal   model   delta    sigma   weight residual
     108.23  114.45   -6.22 1.62e+00 3.81e-01 1.47e+01
  ... (remaining 11199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.17: 4406
       11.17 -    22.35: 500
       22.35 -    33.52: 63
       33.52 -    44.69: 25
       44.69 -    55.86: 4
  Dihedral angle restraints: 4998
    sinusoidal: 2088
      harmonic: 2910
  Sorted by residual:
  dihedral pdb=" CA  GLN B1129 "
           pdb=" C   GLN B1129 "
           pdb=" N   ALA B1130 "
           pdb=" CA  ALA B1130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -124.14  -55.86     0      5.00e+00 4.00e-02 1.25e+02
  dihedral pdb=" CA  ILE A1125 "
           pdb=" C   ILE A1125 "
           pdb=" N   LEU A1126 "
           pdb=" CA  LEU A1126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.47  -44.53     0      5.00e+00 4.00e-02 7.93e+01
  dihedral pdb=" CA  LEU B1126 "
           pdb=" C   LEU B1126 "
           pdb=" N   SER B1127 "
           pdb=" CA  SER B1127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.95  -44.05     0      5.00e+00 4.00e-02 7.76e+01
  ... (remaining 4995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 791
       0.046 -    0.092: 296
       0.092 -    0.139: 94
       0.139 -    0.185: 14
       0.185 -    0.231: 5
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CA  SER B1127 "
            pdb=" N   SER B1127 "
            pdb=" C   SER B1127 "
            pdb=" CB  SER B1127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  ILE B1023 "
            pdb=" CA  ILE B1023 "
            pdb=" CG1 ILE B1023 "
            pdb=" CG2 ILE B1023 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  ILE A1023 "
            pdb=" CA  ILE A1023 "
            pdb=" CG1 ILE A1023 "
            pdb=" CG2 ILE A1023 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1197 not shown)

  Planarity restraints: 1432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B1170 "    0.031 2.00e-02 2.50e+03   3.18e-02 2.53e+01
        pdb=" CG  TRP B1170 "   -0.084 2.00e-02 2.50e+03
        pdb=" CD1 TRP B1170 "    0.045 2.00e-02 2.50e+03
        pdb=" CD2 TRP B1170 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B1170 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B1170 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B1170 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B1170 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B1170 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP B1170 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1170 "   -0.030 2.00e-02 2.50e+03   3.09e-02 2.39e+01
        pdb=" CG  TRP A1170 "    0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1170 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1170 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1170 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1170 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1170 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1170 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1170 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1170 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B1129 "    0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   GLN B1129 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLN B1129 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ALA B1130 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1429 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2152
        2.80 -     3.33: 7635
        3.33 -     3.85: 13569
        3.85 -     4.38: 15627
        4.38 -     4.90: 24977
  Nonbonded interactions: 63960
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B1043 "
            pdb=" OE1 GLU B1173 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR A1043 "
            pdb=" OE1 GLU A1173 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   PHE B 809 "
            pdb=" OG1 THR B 812 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   PHE A 809 "
            pdb=" OG1 THR A 812 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER A 787 "
            pdb=" OD2 ASP A 794 "
     model   vdw
     2.292 3.040
  ... (remaining 63955 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             3.170
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.860
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
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      :  0.007   0.055   8286  Z= 0.463
  Angle     :  1.064  12.515  11204  Z= 0.596
  Chirality :  0.054   0.231   1200
  Planarity :  0.009   0.073   1432
  Dihedral  :  9.436  55.861   3130
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.85 %

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: -3.21 (0.24), residues: 980
  helix: -1.63 (0.19), residues: 436
  sheet: -2.45 (0.49), residues: 112
  loop : -2.47 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.084   0.007   TRP B1170 
 HIS   0.007   0.002   HIS B 752 
 PHE   0.024   0.003   PHE B 750 
 TYR   0.032   0.003   TYR B 917 
 ARG   0.008   0.001   ARG B 940 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  843 LEU cc_start: 0.9058 (tp) cc_final: 0.8791 (tt)
REVERT: A  847 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7361 (mt-10)
REVERT: A  954 SER cc_start: 0.8457 (m) cc_final: 0.8253 (p)
REVERT: A  957 MET cc_start: 0.9455 (mmm) cc_final: 0.9068 (mmm)
REVERT: A  966 TYR cc_start: 0.6365 (m-80) cc_final: 0.6058 (m-80)
REVERT: A 1106 GLU cc_start: 0.8215 (pm20) cc_final: 0.7934 (pm20)
REVERT: A 1169 VAL cc_start: 0.9403 (t) cc_final: 0.9083 (t)
REVERT: B  843 LEU cc_start: 0.9001 (tp) cc_final: 0.8741 (tt)
REVERT: B  847 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7092 (mt-10)
REVERT: B  897 LEU cc_start: 0.7919 (mt) cc_final: 0.7414 (mp)
REVERT: B  954 SER cc_start: 0.8554 (m) cc_final: 0.8350 (p)
REVERT: B  957 MET cc_start: 0.9477 (mmm) cc_final: 0.9085 (mmm)
REVERT: B  966 TYR cc_start: 0.6621 (m-80) cc_final: 0.6228 (m-80)
REVERT: B 1106 GLU cc_start: 0.8184 (pm20) cc_final: 0.7917 (pm20)
REVERT: B 1132 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7549 (tp30)
REVERT: B 1148 MET cc_start: 0.7242 (mtm) cc_final: 0.6627 (ptm)
REVERT: B 1169 VAL cc_start: 0.9387 (t) cc_final: 0.9036 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2357
  time to fit residues: 61.8475
Evaluate side-chains
  107 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:   20.0000
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 57 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
A 804 GLN
A 864 GLN
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 789 HIS
B 804 GLN
B 864 GLN
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1012 HIS
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8286  Z= 0.174
  Angle     :  0.625   9.423  11204  Z= 0.336
  Chirality :  0.042   0.153   1200
  Planarity :  0.006   0.050   1432
  Dihedral  :  6.636  46.959   1104
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.85 %

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: -1.79 (0.26), residues: 980
  helix:  0.13 (0.24), residues: 428
  sheet: -2.16 (0.48), residues: 112
  loop : -2.28 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A1170 
 HIS   0.004   0.001   HIS B 883 
 PHE   0.008   0.001   PHE B 750 
 TYR   0.015   0.002   TYR B 917 
 ARG   0.009   0.001   ARG B 716 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.965 
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: A  714 MET cc_start: 0.8181 (mpp) cc_final: 0.7677 (mpp)
REVERT: A  957 MET cc_start: 0.9463 (mmm) cc_final: 0.9074 (mmm)
REVERT: A  966 TYR cc_start: 0.6301 (m-80) cc_final: 0.6059 (m-80)
REVERT: A 1128 LEU cc_start: 0.8759 (mt) cc_final: 0.8528 (mt)
REVERT: A 1169 VAL cc_start: 0.9272 (t) cc_final: 0.8845 (p)
REVERT: B  714 MET cc_start: 0.8289 (mpp) cc_final: 0.7773 (mpp)
REVERT: B  957 MET cc_start: 0.9473 (mmm) cc_final: 0.9081 (mmm)
REVERT: B  966 TYR cc_start: 0.6528 (m-80) cc_final: 0.6212 (m-80)
REVERT: B 1112 GLU cc_start: 0.9078 (mp0) cc_final: 0.8624 (mp0)
REVERT: B 1169 VAL cc_start: 0.9317 (t) cc_final: 0.8937 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2079
  time to fit residues: 45.3371
Evaluate side-chains
  99 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 60 optimal weight:    0.3980
   chunk 24 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0980
   chunk 96 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 88 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0070
   overall best weight:    1.9002

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

Flipped N/Q/H residues before XYZ refinement:
A 774 HIS
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 774 HIS
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8286  Z= 0.201
  Angle     :  0.617   9.121  11204  Z= 0.330
  Chirality :  0.042   0.155   1200
  Planarity :  0.006   0.048   1432
  Dihedral  :  6.145  47.189   1104
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.61 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

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: -1.29 (0.27), residues: 980
  helix:  0.60 (0.24), residues: 436
  sheet: -1.89 (0.46), residues: 122
  loop : -2.12 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1170 
 HIS   0.003   0.001   HIS B1099 
 PHE   0.013   0.001   PHE A 710 
 TYR   0.019   0.002   TYR A 769 
 ARG   0.004   0.000   ARG B1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.976 
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: A  714 MET cc_start: 0.8321 (mpp) cc_final: 0.7792 (mpp)
REVERT: A  856 TRP cc_start: 0.4329 (p-90) cc_final: 0.3926 (p-90)
REVERT: A  957 MET cc_start: 0.9487 (mmm) cc_final: 0.9075 (mmm)
REVERT: A  966 TYR cc_start: 0.6291 (m-80) cc_final: 0.6053 (m-80)
REVERT: A 1148 MET cc_start: 0.7145 (ptt) cc_final: 0.6843 (ptt)
REVERT: B  714 MET cc_start: 0.8344 (mpp) cc_final: 0.7832 (mpp)
REVERT: B  885 LEU cc_start: 0.8957 (mm) cc_final: 0.8726 (mt)
REVERT: B  905 ASN cc_start: 0.8575 (m110) cc_final: 0.8235 (m110)
REVERT: B  957 MET cc_start: 0.9468 (mmm) cc_final: 0.9051 (mmm)
REVERT: B  966 TYR cc_start: 0.6528 (m-80) cc_final: 0.6217 (m-80)
REVERT: B 1148 MET cc_start: 0.7245 (mtm) cc_final: 0.6900 (ttm)
REVERT: B 1169 VAL cc_start: 0.9399 (t) cc_final: 0.8331 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2179
  time to fit residues: 39.9642
Evaluate side-chains
  94 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 46 optimal weight:    0.4980
   chunk 9 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8286  Z= 0.182
  Angle     :  0.580   9.170  11204  Z= 0.311
  Chirality :  0.042   0.154   1200
  Planarity :  0.005   0.042   1432
  Dihedral  :  5.851  48.781   1104
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

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: -0.83 (0.27), residues: 980
  helix:  1.06 (0.24), residues: 436
  sheet: -1.68 (0.47), residues: 122
  loop : -1.96 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B1189 
 HIS   0.003   0.001   HIS B1012 
 PHE   0.015   0.001   PHE B 741 
 TYR   0.018   0.001   TYR B 917 
 ARG   0.007   0.000   ARG B1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8321 (mpp) cc_final: 0.7855 (mpp)
REVERT: A  856 TRP cc_start: 0.4057 (p-90) cc_final: 0.3729 (p-90)
REVERT: A  957 MET cc_start: 0.9484 (mmm) cc_final: 0.9084 (mmm)
REVERT: A  966 TYR cc_start: 0.6270 (m-80) cc_final: 0.6031 (m-80)
REVERT: A 1060 MET cc_start: 0.8049 (tmm) cc_final: 0.7527 (tmm)
REVERT: A 1148 MET cc_start: 0.6898 (ptt) cc_final: 0.5890 (ptt)
REVERT: A 1173 GLU cc_start: 0.8981 (pm20) cc_final: 0.8694 (pm20)
REVERT: B  714 MET cc_start: 0.8362 (mpp) cc_final: 0.7904 (mpp)
REVERT: B  885 LEU cc_start: 0.8888 (mm) cc_final: 0.8509 (mt)
REVERT: B  905 ASN cc_start: 0.8615 (m110) cc_final: 0.8280 (m110)
REVERT: B  957 MET cc_start: 0.9476 (mmm) cc_final: 0.9073 (mmm)
REVERT: B  966 TYR cc_start: 0.6513 (m-80) cc_final: 0.6202 (m-80)
REVERT: B 1060 MET cc_start: 0.8036 (tmm) cc_final: 0.7379 (tmm)
REVERT: B 1148 MET cc_start: 0.7246 (mtm) cc_final: 0.7025 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2161
  time to fit residues: 39.9708
Evaluate side-chains
  95 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   chunk 70 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8286  Z= 0.147
  Angle     :  0.550   8.853  11204  Z= 0.293
  Chirality :  0.041   0.157   1200
  Planarity :  0.005   0.065   1432
  Dihedral  :  5.523  49.157   1104
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.28), residues: 980
  helix:  1.23 (0.24), residues: 462
  sheet: -1.58 (0.48), residues: 122
  loop : -1.97 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1189 
 HIS   0.002   0.001   HIS A 883 
 PHE   0.006   0.001   PHE B 710 
 TYR   0.020   0.001   TYR A1043 
 ARG   0.006   0.000   ARG A1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8776 (p0) cc_final: 0.6378 (p0)
REVERT: A  714 MET cc_start: 0.8175 (mpp) cc_final: 0.7766 (mpp)
REVERT: A  856 TRP cc_start: 0.4051 (p-90) cc_final: 0.3696 (p-90)
REVERT: A  882 LYS cc_start: 0.8463 (pttt) cc_final: 0.8181 (ptpp)
REVERT: A  957 MET cc_start: 0.9491 (mmm) cc_final: 0.9069 (mmm)
REVERT: A  966 TYR cc_start: 0.6299 (m-80) cc_final: 0.6053 (m-80)
REVERT: A 1148 MET cc_start: 0.6847 (ptt) cc_final: 0.5602 (ptt)
REVERT: B  712 ASP cc_start: 0.8714 (p0) cc_final: 0.5922 (p0)
REVERT: B  714 MET cc_start: 0.8309 (mpp) cc_final: 0.7651 (mpp)
REVERT: B  856 TRP cc_start: 0.3494 (p-90) cc_final: 0.2586 (p-90)
REVERT: B  905 ASN cc_start: 0.8684 (m110) cc_final: 0.8478 (m-40)
REVERT: B  957 MET cc_start: 0.9474 (mmm) cc_final: 0.9048 (mmm)
REVERT: B  966 TYR cc_start: 0.6551 (m-80) cc_final: 0.6232 (m-80)
REVERT: B 1148 MET cc_start: 0.7184 (mtm) cc_final: 0.6943 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2005
  time to fit residues: 37.2938
Evaluate side-chains
  94 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 23 optimal weight:   30.0000
   chunk 94 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 31 optimal weight:    0.2980
   chunk 49 optimal weight:   20.0000
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 905 ASN
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   8286  Z= 0.158
  Angle     :  0.548   9.271  11204  Z= 0.290
  Chirality :  0.041   0.179   1200
  Planarity :  0.005   0.045   1432
  Dihedral  :  5.286  44.364   1104
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.28), residues: 980
  helix:  1.39 (0.24), residues: 460
  sheet: -1.52 (0.49), residues: 122
  loop : -1.83 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1189 
 HIS   0.004   0.001   HIS A1099 
 PHE   0.018   0.001   PHE B 710 
 TYR   0.015   0.001   TYR A1043 
 ARG   0.008   0.000   ARG B1006 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8811 (p0) cc_final: 0.6341 (p0)
REVERT: A  714 MET cc_start: 0.8175 (mpp) cc_final: 0.7701 (mpp)
REVERT: A  856 TRP cc_start: 0.3758 (p-90) cc_final: 0.3538 (p-90)
REVERT: A  882 LYS cc_start: 0.8453 (pttt) cc_final: 0.8170 (ptpp)
REVERT: A  957 MET cc_start: 0.9492 (mmm) cc_final: 0.9065 (mmm)
REVERT: A 1060 MET cc_start: 0.7830 (tmm) cc_final: 0.7500 (tmm)
REVERT: A 1144 LYS cc_start: 0.8771 (tttt) cc_final: 0.8516 (tptp)
REVERT: A 1148 MET cc_start: 0.6813 (ptt) cc_final: 0.6040 (ptt)
REVERT: B  712 ASP cc_start: 0.8787 (p0) cc_final: 0.6344 (p0)
REVERT: B  714 MET cc_start: 0.8211 (mpp) cc_final: 0.7743 (mpp)
REVERT: B  856 TRP cc_start: 0.3390 (p-90) cc_final: 0.2554 (p-90)
REVERT: B  905 ASN cc_start: 0.8644 (m110) cc_final: 0.8425 (m-40)
REVERT: B  917 TYR cc_start: 0.8123 (m-10) cc_final: 0.7900 (m-80)
REVERT: B  957 MET cc_start: 0.9475 (mmm) cc_final: 0.9044 (mmm)
REVERT: B  966 TYR cc_start: 0.6564 (m-80) cc_final: 0.6257 (m-80)
REVERT: B 1060 MET cc_start: 0.7978 (tmm) cc_final: 0.7419 (tmm)
REVERT: B 1148 MET cc_start: 0.7175 (mtm) cc_final: 0.6975 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1913
  time to fit residues: 35.5699
Evaluate side-chains
  95 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0000
   chunk 69 optimal weight:    0.0070
   chunk 53 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 59 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.3004

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8286  Z= 0.163
  Angle     :  0.550   8.774  11204  Z= 0.292
  Chirality :  0.041   0.188   1200
  Planarity :  0.004   0.038   1432
  Dihedral  :  5.178  37.061   1104
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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: -0.15 (0.28), residues: 980
  helix:  1.60 (0.24), residues: 450
  sheet: -1.47 (0.49), residues: 122
  loop : -1.65 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1189 
 HIS   0.002   0.001   HIS B 883 
 PHE   0.016   0.001   PHE B 741 
 TYR   0.022   0.002   TYR A 769 
 ARG   0.006   0.000   ARG B1131 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8856 (p0) cc_final: 0.6383 (p0)
REVERT: A  714 MET cc_start: 0.8196 (mpp) cc_final: 0.7685 (mpp)
REVERT: A  737 LYS cc_start: 0.8759 (mttt) cc_final: 0.8413 (mtpt)
REVERT: A  856 TRP cc_start: 0.3728 (p-90) cc_final: 0.3362 (p-90)
REVERT: A  882 LYS cc_start: 0.8473 (pttt) cc_final: 0.8182 (ptpp)
REVERT: A  905 ASN cc_start: 0.8685 (m110) cc_final: 0.8478 (m-40)
REVERT: A  957 MET cc_start: 0.9493 (mmm) cc_final: 0.9070 (mmm)
REVERT: A 1060 MET cc_start: 0.7986 (tmm) cc_final: 0.7570 (tmm)
REVERT: A 1128 LEU cc_start: 0.7852 (mm) cc_final: 0.7639 (mm)
REVERT: A 1148 MET cc_start: 0.6829 (ptt) cc_final: 0.5645 (ptt)
REVERT: B  712 ASP cc_start: 0.8771 (p0) cc_final: 0.6357 (p0)
REVERT: B  714 MET cc_start: 0.8172 (mpp) cc_final: 0.7740 (mpp)
REVERT: B  856 TRP cc_start: 0.3430 (p-90) cc_final: 0.2573 (p-90)
REVERT: B  905 ASN cc_start: 0.8676 (m110) cc_final: 0.8458 (m-40)
REVERT: B  917 TYR cc_start: 0.8209 (m-10) cc_final: 0.7967 (m-80)
REVERT: B  957 MET cc_start: 0.9477 (mmm) cc_final: 0.9046 (mmm)
REVERT: B  966 TYR cc_start: 0.6549 (m-80) cc_final: 0.6263 (m-80)
REVERT: B 1060 MET cc_start: 0.7994 (tmm) cc_final: 0.7674 (tmm)
REVERT: B 1148 MET cc_start: 0.7226 (mtm) cc_final: 0.7026 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1444
  time to fit residues: 26.9001
Evaluate side-chains
  98 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    0.0000
   chunk 56 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0980
   chunk 8 optimal weight:   30.0000
   chunk 74 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8286  Z= 0.152
  Angle     :  0.543   8.638  11204  Z= 0.284
  Chirality :  0.041   0.166   1200
  Planarity :  0.004   0.038   1432
  Dihedral  :  5.084  41.146   1104
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.28), residues: 980
  helix:  1.80 (0.24), residues: 448
  sheet: -1.29 (0.50), residues: 122
  loop : -1.57 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1189 
 HIS   0.002   0.001   HIS B 909 
 PHE   0.015   0.001   PHE A 739 
 TYR   0.011   0.001   TYR A1043 
 ARG   0.009   0.000   ARG B1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8849 (p0) cc_final: 0.6408 (p0)
REVERT: A  714 MET cc_start: 0.8163 (mpp) cc_final: 0.7649 (mpp)
REVERT: A  737 LYS cc_start: 0.8744 (mttt) cc_final: 0.8439 (mtpt)
REVERT: A  856 TRP cc_start: 0.3685 (p-90) cc_final: 0.3323 (p-90)
REVERT: A  882 LYS cc_start: 0.8461 (pttt) cc_final: 0.8182 (ptpp)
REVERT: A  905 ASN cc_start: 0.8696 (m110) cc_final: 0.8485 (m-40)
REVERT: A  957 MET cc_start: 0.9491 (mmm) cc_final: 0.9065 (mmm)
REVERT: A  966 TYR cc_start: 0.6516 (m-10) cc_final: 0.6277 (m-80)
REVERT: A 1060 MET cc_start: 0.8025 (tmm) cc_final: 0.7554 (tmm)
REVERT: A 1144 LYS cc_start: 0.8757 (tttt) cc_final: 0.8527 (tptp)
REVERT: A 1148 MET cc_start: 0.6792 (ptt) cc_final: 0.5841 (ptt)
REVERT: B  712 ASP cc_start: 0.8808 (p0) cc_final: 0.6331 (p0)
REVERT: B  714 MET cc_start: 0.8143 (mpp) cc_final: 0.7705 (mpp)
REVERT: B  856 TRP cc_start: 0.3459 (p-90) cc_final: 0.2620 (p-90)
REVERT: B  917 TYR cc_start: 0.8160 (m-10) cc_final: 0.7908 (m-80)
REVERT: B  957 MET cc_start: 0.9475 (mmm) cc_final: 0.9041 (mmm)
REVERT: B 1060 MET cc_start: 0.8032 (tmm) cc_final: 0.7692 (tmm)
REVERT: B 1148 MET cc_start: 0.7239 (mtm) cc_final: 0.7027 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1745
  time to fit residues: 33.9693
Evaluate side-chains
  102 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8286  Z= 0.157
  Angle     :  0.552   8.946  11204  Z= 0.287
  Chirality :  0.042   0.169   1200
  Planarity :  0.004   0.038   1432
  Dihedral  :  5.017  39.305   1104
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

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:  0.11 (0.28), residues: 980
  helix:  1.84 (0.24), residues: 446
  sheet: -1.03 (0.52), residues: 118
  loop : -1.61 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1189 
 HIS   0.002   0.001   HIS B 883 
 PHE   0.014   0.001   PHE A 739 
 TYR   0.023   0.001   TYR A 769 
 ARG   0.005   0.000   ARG B1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8872 (p0) cc_final: 0.6448 (p0)
REVERT: A  714 MET cc_start: 0.8200 (mpp) cc_final: 0.7647 (mpp)
REVERT: A  856 TRP cc_start: 0.3641 (p-90) cc_final: 0.3124 (p-90)
REVERT: A  905 ASN cc_start: 0.8701 (m110) cc_final: 0.8485 (m-40)
REVERT: A  957 MET cc_start: 0.9491 (mmm) cc_final: 0.9067 (mmm)
REVERT: A  966 TYR cc_start: 0.6531 (m-10) cc_final: 0.6298 (m-80)
REVERT: A 1060 MET cc_start: 0.8064 (tmm) cc_final: 0.7623 (tmm)
REVERT: A 1144 LYS cc_start: 0.8746 (tttt) cc_final: 0.8532 (tmtt)
REVERT: A 1148 MET cc_start: 0.6795 (ptt) cc_final: 0.6173 (ptt)
REVERT: B  712 ASP cc_start: 0.8823 (p0) cc_final: 0.6312 (p0)
REVERT: B  714 MET cc_start: 0.8118 (mpp) cc_final: 0.7705 (mpp)
REVERT: B  856 TRP cc_start: 0.3345 (p-90) cc_final: 0.2492 (p-90)
REVERT: B  905 ASN cc_start: 0.8695 (m-40) cc_final: 0.8364 (m-40)
REVERT: B  917 TYR cc_start: 0.8215 (m-10) cc_final: 0.7939 (m-80)
REVERT: B  957 MET cc_start: 0.9480 (mmm) cc_final: 0.9054 (mmm)
REVERT: B  966 TYR cc_start: 0.5547 (m-80) cc_final: 0.5258 (m-80)
REVERT: B 1060 MET cc_start: 0.8026 (tmm) cc_final: 0.7678 (tmm)
REVERT: B 1128 LEU cc_start: 0.8676 (mt) cc_final: 0.8263 (mp)
REVERT: B 1148 MET cc_start: 0.7247 (mtm) cc_final: 0.7024 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1662
  time to fit residues: 30.2367
Evaluate side-chains
  95 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0070
   chunk 77 optimal weight:    5.9990
   chunk 8 optimal weight:   30.0000
   chunk 60 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.9804

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 887 HIS
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.4897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8286  Z= 0.152
  Angle     :  0.549   8.924  11204  Z= 0.286
  Chirality :  0.041   0.166   1200
  Planarity :  0.004   0.039   1432
  Dihedral  :  4.976  41.208   1104
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.32 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.28), residues: 980
  helix:  1.94 (0.24), residues: 444
  sheet: -0.98 (0.52), residues: 118
  loop : -1.58 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B1189 
 HIS   0.005   0.001   HIS A 883 
 PHE   0.013   0.001   PHE A 739 
 TYR   0.013   0.001   TYR A1033 
 ARG   0.005   0.000   ARG B1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8791 (p0) cc_final: 0.6337 (p0)
REVERT: A  714 MET cc_start: 0.8163 (mpp) cc_final: 0.7644 (mpp)
REVERT: A  856 TRP cc_start: 0.3616 (p-90) cc_final: 0.3095 (p-90)
REVERT: A  905 ASN cc_start: 0.8687 (m110) cc_final: 0.8487 (m-40)
REVERT: A  957 MET cc_start: 0.9489 (mmm) cc_final: 0.9059 (mmm)
REVERT: A  966 TYR cc_start: 0.6540 (m-10) cc_final: 0.6305 (m-80)
REVERT: A 1060 MET cc_start: 0.8056 (tmm) cc_final: 0.7599 (tmm)
REVERT: A 1144 LYS cc_start: 0.8745 (tttt) cc_final: 0.8521 (tptp)
REVERT: A 1148 MET cc_start: 0.6784 (ptt) cc_final: 0.5898 (ptt)
REVERT: B  712 ASP cc_start: 0.8852 (p0) cc_final: 0.6305 (p0)
REVERT: B  714 MET cc_start: 0.8122 (mpp) cc_final: 0.7677 (mpp)
REVERT: B  856 TRP cc_start: 0.3328 (p-90) cc_final: 0.2438 (p-90)
REVERT: B  905 ASN cc_start: 0.8682 (m-40) cc_final: 0.8358 (m-40)
REVERT: B  917 TYR cc_start: 0.8216 (m-10) cc_final: 0.7921 (m-80)
REVERT: B  957 MET cc_start: 0.9482 (mmm) cc_final: 0.9049 (mmm)
REVERT: B  966 TYR cc_start: 0.5625 (m-80) cc_final: 0.5333 (m-80)
REVERT: B 1060 MET cc_start: 0.8026 (tmm) cc_final: 0.7646 (tmm)
REVERT: B 1148 MET cc_start: 0.7227 (mtm) cc_final: 0.7009 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1785
  time to fit residues: 31.0158
Evaluate side-chains
  91 residues out of total 870 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 23 optimal weight:   20.0000
   chunk 71 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0070
   chunk 79 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0870
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 ASN
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.087363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.070160 restraints weight = 36557.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.072155 restraints weight = 24058.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.073727 restraints weight = 17665.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.5059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8286  Z= 0.144
  Angle     :  0.532   8.731  11204  Z= 0.275
  Chirality :  0.041   0.157   1200
  Planarity :  0.004   0.039   1432
  Dihedral  :  4.837  40.048   1104
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

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:  0.24 (0.29), residues: 980
  helix:  1.98 (0.24), residues: 452
  sheet: -0.95 (0.53), residues: 118
  loop : -1.66 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.011   0.001   PHE A 739 
 TYR   0.021   0.001   TYR B 769 
 ARG   0.004   0.000   ARG A1039 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2056.26 seconds
wall clock time: 37 minutes 32.04 seconds (2252.04 seconds total)