Starting phenix.real_space_refine
on Fri Aug 22 14:02:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jvm_36677/08_2025/8jvm_36677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jvm_36677/08_2025/8jvm_36677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jvm_36677/08_2025/8jvm_36677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jvm_36677/08_2025/8jvm_36677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jvm_36677/08_2025/8jvm_36677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jvm_36677/08_2025/8jvm_36677.cif"
  }
  resolution = 3.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=  -0.003 sd=   0.021
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      15      5.16       5
     C    2310      2.51       5
     N     636      2.21       5
     O     765      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3726
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "F"
      Number of atoms: 1242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1242
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 6, 'TRANS': 159}
    Chain: "J"
      Number of atoms: 1242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1242
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 6, 'TRANS': 159}
    Chain: "Z"
      Number of atoms: 1242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1242
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 6, 'TRANS': 159}
  Time building chain proxies: 1.01, per 1000 atoms: 0.27
  Number of scatterers: 3726
  At special positions: 0
  Unit cell: (63.3778, 65.5262, 157.907, 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      15     16.00
     O     765      8.00
     N     636      7.00
     C    2310      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  - 3.00
        Amino acid           : True  - 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: 0.30
  Conformation dependent library (CDL) restraints added in 151.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  918

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 10 sheets defined
      23.5% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'F' and resid 831 through 866
      removed outlier: 3.637A  pdb=" N   VAL F 835 " --> pdb=" O   LEU F 831 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR F 838 " --> pdb=" O   LYS F 834 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLU F 839 " --> pdb=" O   VAL F 835 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA F 864 " --> pdb=" O   ASN F 860 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL F 865 " --> pdb=" O   ALA F 861 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 918 through 922
      removed outlier: 4.178A  pdb=" N   ASN F 921 " --> pdb=" O   ALA F 918 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 831 through 866
      removed outlier: 4.193A  pdb=" N   VAL J 835 " --> pdb=" O   LEU J 831 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU J 836 " --> pdb=" O   LEU J 832 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG J 844 " --> pdb=" O   ASP J 840 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU J 846 " --> pdb=" O   ALA J 842 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLU J 847 " --> pdb=" O   SER J 843 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA J 864 " --> pdb=" O   ASN J 860 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 907 through 911
    Processing helix  chain 'Z' and resid 832 through 866
      removed outlier: 3.534A  pdb=" N   THR Z 838 " --> pdb=" O   LYS Z 834 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLU Z 839 " --> pdb=" O   VAL Z 835 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA Z 864 " --> pdb=" O   ASN Z 860 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL Z 865 " --> pdb=" O   ALA Z 861 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 882 through 887
    Processing sheet with id=AA2, first strand: chain 'F' and resid 932 through 934
      removed outlier: 6.689A  pdb=" N   LEU F 933 " --> pdb=" O   THR Z 939 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'F' and resid 955 through 957
      removed outlier: 6.486A  pdb=" N   LEU F 955 " --> pdb=" O   ASP Z 961 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'F' and resid 959 through 962
      removed outlier: 5.775A  pdb=" N   ASN F 959 " --> pdb=" O   LEU J 955 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ALA J 957 " --> pdb=" O   ASN F 959 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   ASP F 961 " --> pdb=" O   ALA J 957 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 988 through 989
      removed outlier: 3.647A  pdb=" N   ILE Z 978 " --> pdb=" O   THR J 983 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LEU Z 973 " --> pdb=" O   ASN F 967 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ASN F 969 " --> pdb=" O   LEU Z 973 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASN J 967 " --> pdb=" O   GLY F 971 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   LEU F 973 " --> pdb=" O   ASN J 967 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ASN J 969 " --> pdb=" O   LEU F 973 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   ALA Z 968 " --> pdb=" O   SER J 970 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   THR J 972 " --> pdb=" O   ALA Z 968 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'J' and resid 960 through 962
      removed outlier: 6.341A  pdb=" N   ASN F 967 " --> pdb=" O   ILE J 962 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR Z 983 " --> pdb=" O   SER F 974 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   VAL F 976 " --> pdb=" O   THR Z 983 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'J' and resid 976 through 978
      removed outlier: 5.538A  pdb=" N   THR F 983 " --> pdb=" O   ILE J 978 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'J' and resid 881 through 886
    Processing sheet with id=AA9, first strand: chain 'J' and resid 905 through 906
      removed outlier: 4.156A  pdb=" N   THR J 913 " --> pdb=" O   ASP J 906 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'Z' and resid 881 through 884
      removed outlier: 3.615A  pdb=" N   GLY Z 881 " --> pdb=" O   LEU Z 896 " (cutoff:3.500A)

    112 hydrogen bonds defined for protein.
    318 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: 0.49

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 692
        1.32 -     1.44: 859
        1.44 -     1.57: 2195
        1.57 -     1.69: 4
        1.69 -     1.81: 27
  Bond restraints: 3777
  Sorted by residual:
  bond pdb=" N   PRO Z 945 "
       pdb=" CA  PRO Z 945 "
    ideal  model  delta    sigma   weight residual
    1.469  1.579 -0.110 1.28e-02 6.10e+03 7.39e+01
  bond pdb=" N   ALA Z 946 "
       pdb=" CA  ALA Z 946 "
    ideal  model  delta    sigma   weight residual
    1.457  1.529 -0.072 1.29e-02 6.01e+03 3.10e+01
  bond pdb=" CA  PRO Z 944 "
       pdb=" C   PRO Z 944 "
    ideal  model  delta    sigma   weight residual
    1.517  1.566 -0.049 9.30e-03 1.16e+04 2.73e+01
  bond pdb=" C   PRO Z 945 "
       pdb=" N   ALA Z 946 "
    ideal  model  delta    sigma   weight residual
    1.332  1.394 -0.061 1.40e-02 5.10e+03 1.91e+01
  bond pdb=" C   PRO Z 944 "
       pdb=" O   PRO Z 944 "
    ideal  model  delta    sigma   weight residual
    1.240  1.193  0.048 1.12e-02 7.97e+03 1.82e+01
  ... (remaining 3772 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.98: 5046
        3.98 -     7.96: 57
        7.96 -    11.94: 6
       11.94 -    15.92: 1
       15.92 -    19.90: 2
  Bond angle restraints: 5112
  Sorted by residual:
  angle pdb=" C   PRO Z 944 "
        pdb=" CA  PRO Z 944 "
        pdb=" CB  PRO Z 944 "
      ideal   model   delta    sigma   weight residual
     110.92  128.26  -17.34 1.22e+00 6.72e-01 2.02e+02
  angle pdb=" N   PRO Z 945 "
        pdb=" CA  PRO Z 945 "
        pdb=" C   PRO Z 945 "
      ideal   model   delta    sigma   weight residual
     112.47  132.37  -19.90 2.06e+00 2.36e-01 9.33e+01
  angle pdb=" CA  ASN Z 943 "
        pdb=" C   ASN Z 943 "
        pdb=" N   PRO Z 944 "
      ideal   model   delta    sigma   weight residual
     117.69  125.70   -8.01 9.30e-01 1.16e+00 7.43e+01
  angle pdb=" C   PRO Z 944 "
        pdb=" N   PRO Z 945 "
        pdb=" CA  PRO Z 945 "
      ideal   model   delta    sigma   weight residual
     119.84  129.01   -9.17 1.25e+00 6.40e-01 5.39e+01
  angle pdb=" N   ALA Z 946 "
        pdb=" CA  ALA Z 946 "
        pdb=" C   ALA Z 946 "
      ideal   model   delta    sigma   weight residual
     110.80  125.60  -14.80 2.13e+00 2.20e-01 4.82e+01
  ... (remaining 5107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 2070
       17.81 -    35.62: 185
       35.62 -    53.43: 43
       53.43 -    71.24: 3
       71.24 -    89.05: 3
  Dihedral angle restraints: 2304
    sinusoidal: 888
      harmonic: 1416
  Sorted by residual:
  dihedral pdb=" C   PRO Z 944 "
           pdb=" N   PRO Z 944 "
           pdb=" CA  PRO Z 944 "
           pdb=" CB  PRO Z 944 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -133.09   12.39     0      2.50e+00 1.60e-01 2.46e+01
  dihedral pdb=" CA  ALA Z 899 "
           pdb=" C   ALA Z 899 "
           pdb=" N   ASN Z 900 "
           pdb=" CA  ASN Z 900 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.77  -23.23     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  PRO F 907 "
           pdb=" C   PRO F 907 "
           pdb=" N   ALA F 908 "
           pdb=" CA  ALA F 908 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.56   21.44     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 2301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 478
       0.065 -    0.130: 92
       0.130 -    0.194: 17
       0.194 -    0.259: 2
       0.259 -    0.323: 2
  Chirality restraints: 591
  Sorted by residual:
  chirality pdb=" CA  ALA Z 946 "
            pdb=" N   ALA Z 946 "
            pdb=" C   ALA Z 946 "
            pdb=" CB  ALA Z 946 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.16    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  PRO Z 944 "
            pdb=" N   PRO Z 944 "
            pdb=" C   PRO Z 944 "
            pdb=" CB  PRO Z 944 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CA  GLU J 836 "
            pdb=" N   GLU J 836 "
            pdb=" C   GLU J 836 "
            pdb=" CB  GLU J 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 588 not shown)

  Planarity restraints: 678
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU J 832 "    0.023 2.00e-02 2.50e+03   4.61e-02 2.13e+01
        pdb=" C   LEU J 832 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   LEU J 832 "    0.030 2.00e-02 2.50e+03
        pdb=" N   GLU J 833 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP Z 859 "   -0.023 2.00e-02 2.50e+03   2.51e-02 1.57e+01
        pdb=" CG  TRP Z 859 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP Z 859 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP Z 859 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP Z 859 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP Z 859 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP Z 859 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP Z 859 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP Z 859 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP Z 859 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN Z 943 "    0.016 2.00e-02 2.50e+03   3.22e-02 1.03e+01
        pdb=" C   ASN Z 943 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ASN Z 943 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PRO Z 944 "    0.020 2.00e-02 2.50e+03
  ... (remaining 675 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 156
        2.69 -     3.24: 3970
        3.24 -     3.80: 6002
        3.80 -     4.35: 7491
        4.35 -     4.90: 11942
  Nonbonded interactions: 29561
  Sorted by model distance:
  nonbonded pdb=" O   ASN Z 943 "
            pdb=" C   PRO Z 944 "
     model   vdw
     2.138 3.270
  nonbonded pdb=" O   PRO F 907 "
            pdb=" NH1 ARG J 901 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" O   ALA J 946 "
            pdb=" OG1 THR J 956 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   GLY Z 986 "
            pdb=" OG1 THR Z 987 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER F 883 "
            pdb=" OE2 GLU F 885 "
     model   vdw
     2.203 3.040
  ... (remaining 29556 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
  selection = chain 'Z'
}

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:             4.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.260
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5528
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      :  0.006   0.110   3777  Z= 0.369
  Angle     :  1.085  19.900   5112  Z= 0.673
  Chirality :  0.056   0.323    591
  Planarity :  0.006   0.052    678
  Dihedral  : 14.544  89.053   1386
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 27.03
  Ramachandran Plot:
    Outliers :  1.63 %
    Allowed  : 16.26 %
    Favored  : 82.11 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  1.75 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.56 (0.34), residues: 492
  helix:  0.67 (0.53), residues: 98
  sheet: -2.56 (0.70), residues: 48
  loop : -3.57 (0.28), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG J 901 
 TYR   0.010   0.002   TYR Z 876 
 PHE   0.022   0.002   PHE Z 848 
 TRP   0.068   0.003   TRP Z 859 
 HIS   0.001   0.000   HIS F 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 3777)
  covalent geometry    : angle       1.08488 ( 5112)
  hydrogen bonds       : bond        0.14041 (  112)
  hydrogen bonds       : angle       7.30385 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Z  976 VAL cc_start: 0.5104 (t) cc_final: 0.4797 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 90
  average time/residue: 0.0786
  time to fit residues: 8.5109
Evaluate side-chains
  68 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** J 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 900 ASN
Z 959 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.142208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.134618 restraints weight = 15941.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.136273 restraints weight = 10816.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.137489 restraints weight = 7748.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.138412 restraints weight = 5729.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.138934 restraints weight = 4341.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.4464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5531
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3777  Z= 0.165
  Angle     :  0.772   7.045   5112  Z= 0.407
  Chirality :  0.046   0.225    591
  Planarity :  0.006   0.080    678
  Dihedral  :  7.423  53.478    517
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 14.63 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.53 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.32 (0.34), residues: 492
  helix:  1.14 (0.50), residues: 98
  sheet: -2.53 (0.70), residues: 48
  loop : -3.47 (0.28), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 932 
 TYR   0.005   0.001   TYR J 876 
 PHE   0.019   0.002   PHE Z 848 
 TRP   0.027   0.002   TRP Z 859 
 HIS   0.011   0.003   HIS J 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3777)
  covalent geometry    : angle       0.77166 ( 5112)
  hydrogen bonds       : bond        0.04863 (  112)
  hydrogen bonds       : angle       5.97823 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Z  832 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6700 (pp)
  outliers start: 10
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1016
  time to fit residues: 9.5041
Evaluate side-chains
  75 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  865 VAL
Chi-restraints excluded: chain Z residue  924 PHE
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0000
   chunk 6 optimal weight:    0.0370
   chunk 17 optimal weight:    0.4980
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0000
   overall best weight:    0.2266

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

Flipped N/Q/H residues before XYZ refinement:
F 922 GLN
J 875 HIS
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.144889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.137663 restraints weight = 16057.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.139282 restraints weight = 10762.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.140528 restraints weight = 7563.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.141398 restraints weight = 5487.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.142046 restraints weight = 4147.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5379
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3777  Z= 0.137
  Angle     :  0.718   6.990   5112  Z= 0.375
  Chirality :  0.045   0.232    591
  Planarity :  0.006   0.097    678
  Dihedral  :  6.782  49.467    517
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 13.21 %
    Favored  : 86.18 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.79 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.99 (0.35), residues: 492
  helix:  1.60 (0.48), residues: 94
  sheet: -2.57 (0.67), residues: 44
  loop : -3.22 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 932 
 TYR   0.021   0.003   TYR Z 876 
 PHE   0.013   0.002   PHE Z 848 
 TRP   0.025   0.002   TRP Z 859 
 HIS   0.009   0.002   HIS J 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3777)
  covalent geometry    : angle       0.71837 ( 5112)
  hydrogen bonds       : bond        0.04527 (  112)
  hydrogen bonds       : angle       5.59720 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  915 MET cc_start: 0.6375 (ppp) cc_final: 0.5791 (ppp)
REVERT: Z  832 LEU cc_start: 0.7167 (mp) cc_final: 0.6717 (pp)
  outliers start: 11
  outliers final: 5
  residues processed: 85
  average time/residue: 0.0925
  time to fit residues: 9.2986
Evaluate side-chains
  73 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain Z residue  865 VAL
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0870
   chunk 31 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
F 922 GLN
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.141471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.133888 restraints weight = 15846.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.135572 restraints weight = 10647.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.136799 restraints weight = 7494.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.137711 restraints weight = 5536.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.138234 restraints weight = 4162.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5543
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3777  Z= 0.171
  Angle     :  0.759   6.945   5112  Z= 0.402
  Chirality :  0.046   0.241    591
  Planarity :  0.007   0.105    678
  Dihedral  :  6.904  46.976    517
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 15.45 %
    Favored  : 83.94 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.05 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.09 (0.35), residues: 492
  helix:  1.36 (0.50), residues: 95
  sheet: -2.59 (0.69), residues: 44
  loop : -3.25 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Z 932 
 TYR   0.007   0.002   TYR J 876 
 PHE   0.032   0.003   PHE Z 848 
 TRP   0.011   0.001   TRP Z 859 
 HIS   0.002   0.001   HIS J 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3777)
  covalent geometry    : angle       0.75928 ( 5112)
  hydrogen bonds       : bond        0.04691 (  112)
  hydrogen bonds       : angle       5.92871 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Z  832 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6709 (pp)
  outliers start: 13
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0873
  time to fit residues: 8.4888
Evaluate side-chains
  81 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain J residue  832 LEU
Chi-restraints excluded: chain J residue  838 THR
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  865 VAL
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
F 900 ASN
F 922 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.141188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.133445 restraints weight = 15628.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.135047 restraints weight = 10644.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.136194 restraints weight = 7620.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.137088 restraints weight = 5679.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.137747 restraints weight = 4347.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.4438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5604
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3777  Z= 0.183
  Angle     :  0.799   7.629   5112  Z= 0.416
  Chirality :  0.047   0.258    591
  Planarity :  0.007   0.108    678
  Dihedral  :  6.874  43.855    515
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 15.24 %
    Favored  : 84.15 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.55 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.24 (0.35), residues: 492
  helix:  1.03 (0.50), residues: 94
  sheet: -2.54 (0.71), residues: 44
  loop : -3.29 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Z 932 
 TYR   0.011   0.002   TYR Z 876 
 PHE   0.028   0.002   PHE Z 848 
 TRP   0.014   0.002   TRP Z 859 
 HIS   0.003   0.001   HIS Z 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 3777)
  covalent geometry    : angle       0.79896 ( 5112)
  hydrogen bonds       : bond        0.04686 (  112)
  hydrogen bonds       : angle       6.03952 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  862 MET cc_start: 0.6986 (mpp) cc_final: 0.6288 (mpp)
REVERT: Z  832 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6667 (pp)
  outliers start: 15
  outliers final: 12
  residues processed: 84
  average time/residue: 0.0895
  time to fit residues: 8.8881
Evaluate side-chains
  82 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  952 ASP
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain J residue  832 LEU
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain J residue  897 VAL
Chi-restraints excluded: chain J residue  905 ILE
Chi-restraints excluded: chain J residue  928 VAL
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  865 VAL
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0870
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0030
   overall best weight:    0.4168

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

Flipped N/Q/H residues before XYZ refinement:
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 875 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.143256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.135404 restraints weight = 15744.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.137046 restraints weight = 10627.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.138283 restraints weight = 7474.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.139173 restraints weight = 5448.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.139744 restraints weight = 4144.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.4467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5506
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3777  Z= 0.147
  Angle     :  0.734   6.596   5112  Z= 0.382
  Chirality :  0.045   0.249    591
  Planarity :  0.006   0.113    678
  Dihedral  :  6.564  41.748    515
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 19.46
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 14.02 %
    Favored  : 85.37 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.06 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.13 (0.35), residues: 492
  helix:  1.22 (0.50), residues: 94
  sheet: -2.41 (0.72), residues: 44
  loop : -3.26 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Z 932 
 TYR   0.006   0.001   TYR Z 876 
 PHE   0.027   0.002   PHE Z 848 
 TRP   0.021   0.002   TRP F 859 
 HIS   0.002   0.001   HIS Z 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3777)
  covalent geometry    : angle       0.73360 ( 5112)
  hydrogen bonds       : bond        0.04571 (  112)
  hydrogen bonds       : angle       5.78939 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  862 MET cc_start: 0.7171 (mpp) cc_final: 0.6340 (mpp)
REVERT: Z  832 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6602 (pp)
  outliers start: 17
  outliers final: 12
  residues processed: 81
  average time/residue: 0.0810
  time to fit residues: 7.9484
Evaluate side-chains
  81 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain F residue  966 VAL
Chi-restraints excluded: chain J residue  832 LEU
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain J residue  897 VAL
Chi-restraints excluded: chain J residue  928 VAL
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  865 VAL
Chi-restraints excluded: chain Z residue  905 ILE
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.141790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.133635 restraints weight = 16132.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.135248 restraints weight = 10975.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.136457 restraints weight = 7794.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.137356 restraints weight = 5801.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.137942 restraints weight = 4448.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5581
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3777  Z= 0.167
  Angle     :  0.788   8.446   5112  Z= 0.412
  Chirality :  0.047   0.259    591
  Planarity :  0.006   0.113    678
  Dihedral  :  6.658  41.502    515
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 15.45 %
    Favored  : 83.94 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.31 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.14 (0.35), residues: 492
  helix:  1.28 (0.49), residues: 94
  sheet: -2.36 (0.74), residues: 44
  loop : -3.30 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG Z 844 
 TYR   0.005   0.001   TYR J 876 
 PHE   0.027   0.002   PHE Z 848 
 TRP   0.020   0.002   TRP Z 859 
 HIS   0.002   0.001   HIS Z 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3777)
  covalent geometry    : angle       0.78752 ( 5112)
  hydrogen bonds       : bond        0.04763 (  112)
  hydrogen bonds       : angle       5.87608 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  862 MET cc_start: 0.7272 (mpp) cc_final: 0.6930 (mpp)
REVERT: Z  832 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6640 (pp)
  outliers start: 18
  outliers final: 13
  residues processed: 83
  average time/residue: 0.0847
  time to fit residues: 8.4305
Evaluate side-chains
  84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain F residue  966 VAL
Chi-restraints excluded: chain J residue  832 LEU
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain J residue  897 VAL
Chi-restraints excluded: chain J residue  928 VAL
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  865 VAL
Chi-restraints excluded: chain Z residue  905 ILE
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Chi-restraints excluded: chain Z residue  987 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0050
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
F 894 GLN
F 922 GLN
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.142118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.133924 restraints weight = 15984.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.135484 restraints weight = 10834.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.136718 restraints weight = 7744.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.137607 restraints weight = 5744.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.138198 restraints weight = 4427.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.4441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5561
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3777  Z= 0.159
  Angle     :  0.775   6.885   5112  Z= 0.405
  Chirality :  0.047   0.254    591
  Planarity :  0.006   0.114    678
  Dihedral  :  6.626  41.382    515
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 15.85 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 24.06 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.14 (0.35), residues: 492
  helix:  1.43 (0.50), residues: 94
  sheet: -2.41 (0.74), residues: 44
  loop : -3.34 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Z 932 
 TYR   0.005   0.001   TYR J 876 
 PHE   0.026   0.002   PHE Z 848 
 TRP   0.012   0.001   TRP Z 859 
 HIS   0.002   0.001   HIS J 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3777)
  covalent geometry    : angle       0.77538 ( 5112)
  hydrogen bonds       : bond        0.04682 (  112)
  hydrogen bonds       : angle       5.82282 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  862 MET cc_start: 0.7280 (mpp) cc_final: 0.6832 (mpp)
REVERT: Z  832 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6594 (pp)
  outliers start: 17
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0815
  time to fit residues: 8.2300
Evaluate side-chains
  83 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  952 ASP
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain F residue  966 VAL
Chi-restraints excluded: chain J residue  832 LEU
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain J residue  897 VAL
Chi-restraints excluded: chain J residue  928 VAL
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  846 GLU
Chi-restraints excluded: chain Z residue  905 ILE
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Chi-restraints excluded: chain Z residue  987 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0670
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
F 894 GLN
F 922 GLN
J 860 ASN
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.142551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.134338 restraints weight = 15871.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.135962 restraints weight = 10846.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.137177 restraints weight = 7790.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.138055 restraints weight = 5817.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.138616 restraints weight = 4516.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.4444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5556
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3777  Z= 0.161
  Angle     :  0.810   8.396   5112  Z= 0.418
  Chirality :  0.047   0.260    591
  Planarity :  0.007   0.116    678
  Dihedral  :  6.589  41.153    515
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 20.82
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 14.63 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.31 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.13 (0.35), residues: 492
  helix:  1.53 (0.51), residues: 93
  sheet: -2.34 (0.75), residues: 44
  loop : -3.36 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG J 901 
 TYR   0.009   0.002   TYR F 876 
 PHE   0.024   0.002   PHE Z 848 
 TRP   0.028   0.002   TRP F 859 
 HIS   0.001   0.001   HIS J 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3777)
  covalent geometry    : angle       0.80964 ( 5112)
  hydrogen bonds       : bond        0.04780 (  112)
  hydrogen bonds       : angle       5.74540 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  862 MET cc_start: 0.7282 (mpp) cc_final: 0.6776 (mpp)
REVERT: Z  832 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6555 (pp)
  outliers start: 15
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0901
  time to fit residues: 8.3840
Evaluate side-chains
  78 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain F residue  966 VAL
Chi-restraints excluded: chain J residue  832 LEU
Chi-restraints excluded: chain J residue  840 ASP
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain J residue  897 VAL
Chi-restraints excluded: chain J residue  928 VAL
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  846 GLU
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Chi-restraints excluded: chain Z residue  987 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0770
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0170
   chunk 25 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 40 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.2976

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

Flipped N/Q/H residues before XYZ refinement:
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.143627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.135556 restraints weight = 16027.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.137244 restraints weight = 10795.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.138465 restraints weight = 7638.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.139193 restraints weight = 5652.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.139918 restraints weight = 4485.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5488
moved from start:          0.4097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3777  Z= 0.152
  Angle     :  0.808   8.529   5112  Z= 0.417
  Chirality :  0.046   0.162    591
  Planarity :  0.006   0.118    678
  Dihedral  :  6.420  39.421    515
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 20.01
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 14.43 %
    Favored  : 85.16 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 27.57 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.35), residues: 492
  helix:  1.45 (0.50), residues: 94
  sheet: -2.11 (0.78), residues: 44
  loop : -3.41 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG J 901 
 TYR   0.010   0.002   TYR Z 876 
 PHE   0.023   0.002   PHE Z 848 
 TRP   0.026   0.002   TRP Z 859 
 HIS   0.002   0.001   HIS J 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3777)
  covalent geometry    : angle       0.80821 ( 5112)
  hydrogen bonds       : bond        0.04662 (  112)
  hydrogen bonds       : angle       5.63087 (  318)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  862 MET cc_start: 0.7372 (mpp) cc_final: 0.6855 (mpp)
REVERT: Z  832 LEU cc_start: 0.6954 (mp) cc_final: 0.6532 (pp)
  outliers start: 12
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0814
  time to fit residues: 8.0395
Evaluate side-chains
  75 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  963 SER
Chi-restraints excluded: chain F residue  966 VAL
Chi-restraints excluded: chain J residue  832 LEU
Chi-restraints excluded: chain J residue  854 ASP
Chi-restraints excluded: chain J residue  897 VAL
Chi-restraints excluded: chain J residue  928 VAL
Chi-restraints excluded: chain Z residue  846 GLU
Chi-restraints excluded: chain Z residue  905 ILE
Chi-restraints excluded: chain Z residue  943 ASN
Chi-restraints excluded: chain Z residue  944 PRO
Chi-restraints excluded: chain Z residue  987 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0770
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
J 860 ASN
** J 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.143461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.136024 restraints weight = 15469.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.137532 restraints weight = 10442.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.138466 restraints weight = 7401.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.139403 restraints weight = 5660.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.139910 restraints weight = 4322.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.4460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5514
moved from start:          0.4180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3777  Z= 0.164
  Angle     :  0.822   8.388   5112  Z= 0.422
  Chirality :  0.046   0.153    591
  Planarity :  0.006   0.117    678
  Dihedral  :  6.526  40.404    515
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 20.82
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 14.84 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 28.07 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.34), residues: 492
  helix:  1.17 (0.51), residues: 94
  sheet: -2.12 (0.78), residues: 44
  loop : -3.46 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J 901 
 TYR   0.012   0.002   TYR Z 876 
 PHE   0.024   0.002   PHE Z 848 
 TRP   0.026   0.002   TRP Z 859 
 HIS   0.002   0.001   HIS J 875 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3777)
  covalent geometry    : angle       0.82221 ( 5112)
  hydrogen bonds       : bond        0.04772 (  112)
  hydrogen bonds       : angle       5.80606 (  318)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1014.22 seconds
wall clock time: 18 minutes 12.98 seconds (1092.98 seconds total)