Starting phenix.real_space_refine
on Wed Mar 12 14:43:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j88_36063/03_2025/8j88_36063.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j88_36063/03_2025/8j88_36063.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j88_36063/03_2025/8j88_36063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j88_36063/03_2025/8j88_36063.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j88_36063/03_2025/8j88_36063.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j88_36063/03_2025/8j88_36063.cif"
  }
  resolution = 3.49
  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=   0.005
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      22      5.16       5
     C    5058      2.51       5
     N    1346      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7846
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3923
          Classifications: {'peptide': 477}
          Link IDs: {'PTRANS': 22, 'TRANS': 454}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.14, per 1000 atoms: 1.04
  Number of scatterers: 7846
  At special positions: 0
  Unit cell: (148.57, 77.19, 108.73, 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      22     16.00
     O    1420      8.00
     N    1346      7.00
     C    5058      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: 1.84
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1812

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      47.3% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 716 through 729
      removed outlier: 3.720A  pdb=" N   LYS A 720 " --> pdb=" O   ARG A 716 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 724 " --> pdb=" O   LYS A 720 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 725 " --> pdb=" O   ILE A 721 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL A 726 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 750
    Processing helix  chain 'A' and resid 754 through 766
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 3.668A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 821
    Processing helix  chain 'A' and resid 866 through 877
    Processing helix  chain 'A' and resid 882 through 893
      removed outlier: 3.594A  pdb=" N   LEU A 886 " --> pdb=" O   LYS A 882 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS A 891 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   HIS A 892 " --> pdb=" O   TYR A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 953
      removed outlier: 3.695A  pdb=" N   TYR A 946 " --> pdb=" O   PRO A 942 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE A 947 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLU A 948 " --> pdb=" O   VAL A 944 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS A 951 " --> pdb=" O   ILE A 947 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   SER A 953 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 960
      removed outlier: 3.572A  pdb=" N   THR A 958 " --> pdb=" O   SER A 954 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   PHE A 959 " --> pdb=" O   ASN A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 981
      No H-bonds generated for 'chain 'A' and resid 979 through 981'
    Processing helix  chain 'A' and resid 982 through 987
      removed outlier: 4.381A  pdb=" N   VAL A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1003
    Processing helix  chain 'A' and resid 1028 through 1070
      Proline residue:  A1037  - end of helix
      removed outlier: 3.771A  pdb=" N   GLN A1044 " --> pdb=" O   ARG A1040 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU A1056 " --> pdb=" O   ALA A1052 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASN A1069 " --> pdb=" O   VAL A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1089
      removed outlier: 3.604A  pdb=" N   LEU A1089 " --> pdb=" O   ALA A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.502A  pdb=" N   ASN A1114 " --> pdb=" O   ILE A1110 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN A1115 " --> pdb=" O   GLU A1111 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLN A1119 " --> pdb=" O   GLN A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1133
      removed outlier: 3.805A  pdb=" N   LEU A1133 " --> pdb=" O   ALA A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1158
      removed outlier: 3.674A  pdb=" N   ILE A1145 " --> pdb=" O   ARG A1141 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS A1146 " --> pdb=" O   VAL A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1187
      removed outlier: 3.518A  pdb=" N   LEU A1171 " --> pdb=" O   ALA A1167 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A1172 " --> pdb=" O   SER A1168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 717 through 729
      removed outlier: 3.673A  pdb=" N   GLY B 724 " --> pdb=" O   LYS B 720 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY B 725 " --> pdb=" O   ILE B 721 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL B 726 " --> pdb=" O   LEU B 722 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 750
    Processing helix  chain 'B' and resid 754 through 766
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 3.669A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 821
    Processing helix  chain 'B' and resid 866 through 877
    Processing helix  chain 'B' and resid 882 through 893
      removed outlier: 3.594A  pdb=" N   LEU B 886 " --> pdb=" O   LYS B 882 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS B 891 " --> pdb=" O   HIS B 887 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   HIS B 892 " --> pdb=" O   TYR B 888 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 953
      removed outlier: 3.695A  pdb=" N   TYR B 946 " --> pdb=" O   PRO B 942 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE B 947 " --> pdb=" O   THR B 943 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLU B 948 " --> pdb=" O   VAL B 944 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS B 951 " --> pdb=" O   ILE B 947 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   SER B 953 " --> pdb=" O   SER B 949 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 953 through 960
      removed outlier: 3.572A  pdb=" N   THR B 958 " --> pdb=" O   SER B 954 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   PHE B 959 " --> pdb=" O   ASN B 955 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 979 through 981
      No H-bonds generated for 'chain 'B' and resid 979 through 981'
    Processing helix  chain 'B' and resid 982 through 987
      removed outlier: 4.381A  pdb=" N   VAL B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 998 through 1003
    Processing helix  chain 'B' and resid 1028 through 1070
      Proline residue:  B1037  - end of helix
      removed outlier: 3.771A  pdb=" N   GLN B1044 " --> pdb=" O   ARG B1040 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU B1056 " --> pdb=" O   ALA B1052 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASN B1069 " --> pdb=" O   VAL B1065 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1084 through 1089
      removed outlier: 3.603A  pdb=" N   LEU B1089 " --> pdb=" O   ALA B1085 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1119
      removed outlier: 3.502A  pdb=" N   ASN B1114 " --> pdb=" O   ILE B1110 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN B1115 " --> pdb=" O   GLU B1111 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLN B1119 " --> pdb=" O   GLN B1115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1129 through 1133
      removed outlier: 3.805A  pdb=" N   LEU B1133 " --> pdb=" O   ALA B1130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1134 through 1158
      removed outlier: 3.673A  pdb=" N   ILE B1145 " --> pdb=" O   ARG B1141 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LYS B1146 " --> pdb=" O   VAL B1142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1187
      removed outlier: 3.519A  pdb=" N   LEU B1171 " --> pdb=" O   ALA B1167 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU B1172 " --> pdb=" O   SER B1168 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 736 through 737
      removed outlier: 3.951A  pdb=" N   GLN A 804 " --> pdb=" O   ILE A 780 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 827
    Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913
      removed outlier: 3.689A  pdb=" N   PHE A 913 " --> pdb=" O   TYR A 916 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   TYR A 917 " --> pdb=" O   LEU A1009 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER A 919 " --> pdb=" O   ASN A1007 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASN A1007 " --> pdb=" O   SER A 919 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 926
      removed outlier: 6.120A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   SER A 926 " --> pdb=" O   ILE A 931 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE A 931 " --> pdb=" O   SER A 926 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 934 " --> pdb=" O   ILE A 974 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ILE A 974 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1015 through 1016
    Processing sheet with id=AA6, first strand: chain 'B' and resid 736 through 737
      removed outlier: 3.951A  pdb=" N   GLN B 804 " --> pdb=" O   ILE B 780 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 826 through 827
    Processing sheet with id=AA8, first strand: chain 'B' and resid 909 through 913
      removed outlier: 3.689A  pdb=" N   PHE B 913 " --> pdb=" O   TYR B 916 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   TYR B 917 " --> pdb=" O   LEU B1009 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER B 919 " --> pdb=" O   ASN B1007 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASN B1007 " --> pdb=" O   SER B 919 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 922 through 926
      removed outlier: 6.121A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER B 926 " --> pdb=" O   ILE B 931 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE B 931 " --> pdb=" O   SER B 926 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 934 " --> pdb=" O   ILE B 974 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ILE B 974 " --> pdb=" O   ILE B 934 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1015 through 1016

    288 hydrogen bonds defined for protein.
    810 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2524
        1.35 -     1.46: 1928
        1.46 -     1.58: 3554
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 8044
  Sorted by residual:
  bond pdb=" C   SER B1162 "
       pdb=" N   PRO B1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.69e+00
  bond pdb=" C   SER A1162 "
       pdb=" N   PRO A1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.030 2.34e-02 1.83e+03 1.59e+00
  bond pdb=" C   ARG A 900 "
       pdb=" N   PRO A 901 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.25e-02 6.40e+03 9.81e-01
  bond pdb=" C   ARG B 900 "
       pdb=" N   PRO B 901 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.25e-02 6.40e+03 9.29e-01
  bond pdb=" C   LEU A 937 "
       pdb=" N   PRO A 938 "
    ideal  model  delta    sigma   weight residual
    1.331  1.343 -0.011 1.21e-02 6.83e+03 8.76e-01
  ... (remaining 8039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 10710
        1.85 -     3.70: 138
        3.70 -     5.55: 16
        5.55 -     7.41: 2
        7.41 -     9.26: 8
  Bond angle restraints: 10874
  Sorted by residual:
  angle pdb=" CB  MET B 957 "
        pdb=" CG  MET B 957 "
        pdb=" SD  MET B 957 "
      ideal   model   delta    sigma   weight residual
     112.70  121.96   -9.26 3.00e+00 1.11e-01 9.52e+00
  angle pdb=" CB  MET A 957 "
        pdb=" CG  MET A 957 "
        pdb=" SD  MET A 957 "
      ideal   model   delta    sigma   weight residual
     112.70  121.93   -9.23 3.00e+00 1.11e-01 9.48e+00
  angle pdb=" CA  LEU B1159 "
        pdb=" CB  LEU B1159 "
        pdb=" CG  LEU B1159 "
      ideal   model   delta    sigma   weight residual
     116.30  125.37   -9.07 3.50e+00 8.16e-02 6.71e+00
  angle pdb=" CA  LEU A1159 "
        pdb=" CB  LEU A1159 "
        pdb=" CG  LEU A1159 "
      ideal   model   delta    sigma   weight residual
     116.30  125.34   -9.04 3.50e+00 8.16e-02 6.68e+00
  angle pdb=" CA  LEU B1126 "
        pdb=" CB  LEU B1126 "
        pdb=" CG  LEU B1126 "
      ideal   model   delta    sigma   weight residual
     116.30  125.00   -8.70 3.50e+00 8.16e-02 6.18e+00
  ... (remaining 10869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.66: 4413
       15.66 -    31.31: 353
       31.31 -    46.97: 74
       46.97 -    62.62: 4
       62.62 -    78.28: 6
  Dihedral angle restraints: 4850
    sinusoidal: 2026
      harmonic: 2824
  Sorted by residual:
  dihedral pdb=" CA  THR A1123 "
           pdb=" C   THR A1123 "
           pdb=" N   TYR A1124 "
           pdb=" CA  TYR A1124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  THR B1123 "
           pdb=" C   THR B1123 "
           pdb=" N   TYR B1124 "
           pdb=" CA  TYR B1124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  PRO B 938 "
           pdb=" C   PRO B 938 "
           pdb=" N   LEU B 939 "
           pdb=" CA  LEU B 939 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.90  -15.10     0      5.00e+00 4.00e-02 9.12e+00
  ... (remaining 4847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 676
       0.028 -    0.056: 314
       0.056 -    0.084: 103
       0.084 -    0.112: 50
       0.112 -    0.141: 17
  Chirality restraints: 1160
  Sorted by residual:
  chirality pdb=" CB  VAL A 838 "
            pdb=" CA  VAL A 838 "
            pdb=" CG1 VAL A 838 "
            pdb=" CG2 VAL A 838 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.77    0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CB  VAL B 838 "
            pdb=" CA  VAL B 838 "
            pdb=" CG1 VAL B 838 "
            pdb=" CG2 VAL B 838 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.77    0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  SER B1162 "
            pdb=" N   SER B1162 "
            pdb=" C   SER B1162 "
            pdb=" CB  SER B1162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 1157 not shown)

  Planarity restraints: 1388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 937 "    0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO B 938 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 938 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 938 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 937 "   -0.030 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO A 938 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 938 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 938 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 900 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO B 901 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 901 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 901 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1385 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 662
        2.74 -     3.28: 7950
        3.28 -     3.82: 12752
        3.82 -     4.36: 14599
        4.36 -     4.90: 24565
  Nonbonded interactions: 60528
  Sorted by model distance:
  nonbonded pdb=" OG  SER B1071 "
            pdb=" OE1 GLU B1073 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OG  SER A1071 "
            pdb=" OE1 GLU A1073 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OH  TYR B1043 "
            pdb=" OE1 GLU B1173 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OH  TYR A1043 "
            pdb=" OE1 GLU A1173 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   THR A1100 "
            pdb=" OG  SER A1104 "
     model   vdw
     2.285 3.040
  ... (remaining 60523 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: 0.04
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     24.080
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:3.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5784
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      :  0.002   0.030   8044  Z= 0.129
  Angle     :  0.562   9.258  10874  Z= 0.290
  Chirality :  0.040   0.141   1160
  Planarity :  0.004   0.047   1388
  Dihedral  : 11.869  78.275   3038
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.27), residues: 950
  helix: -0.25 (0.27), residues: 374
  sheet: -0.36 (0.53), residues: 124
  loop : -0.94 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1078 
 PHE   0.017   0.001   PHE B 913 
 TYR   0.019   0.001   TYR B1079 
 ARG   0.004   0.000   ARG B1039 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.884 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1964
  time to fit residues: 20.0331
Evaluate side-chains
  51 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0670
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    1.1522

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

Flipped N/Q/H residues before XYZ refinement:
** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1012 HIS
B1014 ASN
** B1192 HIS ** 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 = 0.4755 r_free = 0.4755 target = 0.123961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.107420 restraints weight = 41652.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.4396 rms_B_bonded: 6.85
r_work (final): 0.4396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6109
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8044  Z= 0.203
  Angle     :  0.602   8.717  10874  Z= 0.307
  Chirality :  0.043   0.137   1160
  Planarity :  0.005   0.043   1388
  Dihedral  :  4.147  19.094   1072
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  6.40 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.28), residues: 950
  helix:  0.63 (0.27), residues: 390
  sheet: -0.25 (0.52), residues: 126
  loop : -1.13 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 856 
 HIS   0.006   0.001   HIS A1051 
 PHE   0.014   0.001   PHE B 913 
 TYR   0.013   0.002   TYR B1043 
 ARG   0.014   0.001   ARG B1039 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.865 
Fit side-chains
REVERT: B  903 ASN cc_start: 0.8071 (m-40) cc_final: 0.7788 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 62
  average time/residue: 0.1723
  time to fit residues: 15.9366
Evaluate side-chains
  53 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain B residue  750 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0470
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.0084

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

Flipped N/Q/H residues before XYZ refinement:
A 930 ASN
** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
A1014 ASN
B 753 HIS
** B1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.121805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.104687 restraints weight = 42166.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.4286 rms_B_bonded: 7.35
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8044  Z= 0.173
  Angle     :  0.539   8.808  10874  Z= 0.276
  Chirality :  0.042   0.135   1160
  Planarity :  0.004   0.040   1388
  Dihedral  :  4.169  21.956   1072
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.60 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.28), residues: 950
  helix:  0.94 (0.28), residues: 392
  sheet: -0.65 (0.49), residues: 128
  loop : -1.14 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 856 
 HIS   0.005   0.001   HIS A1051 
 PHE   0.021   0.001   PHE B 913 
 TYR   0.012   0.002   TYR A1038 
 ARG   0.006   0.001   ARG B1039 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.6281 (mp) cc_final: 0.6043 (tp)
REVERT: A  957 MET cc_start: 0.6236 (tpt) cc_final: 0.5802 (mmm)
REVERT: B  957 MET cc_start: 0.6474 (tpt) cc_final: 0.5991 (mmm)
REVERT: B 1026 ASN cc_start: 0.8215 (p0) cc_final: 0.7958 (p0)
  outliers start: 7
  outliers final: 3
  residues processed: 60
  average time/residue: 0.1756
  time to fit residues: 15.7272
Evaluate side-chains
  47 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain B residue 1047 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 72 optimal weight:    0.3980
   chunk 78 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0270
   chunk 53 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
A1014 ASN
** B1001 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 = 0.4714 r_free = 0.4714 target = 0.123205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.106215 restraints weight = 41351.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.4316 rms_B_bonded: 7.31
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6142
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8044  Z= 0.129
  Angle     :  0.500   8.342  10874  Z= 0.253
  Chirality :  0.041   0.136   1160
  Planarity :  0.004   0.041   1388
  Dihedral  :  3.903  21.455   1072
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.14 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.28), residues: 950
  helix:  1.36 (0.29), residues: 380
  sheet: -0.55 (0.50), residues: 128
  loop : -1.18 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 856 
 HIS   0.004   0.001   HIS A1051 
 PHE   0.027   0.001   PHE A1164 
 TYR   0.015   0.001   TYR B1029 
 ARG   0.003   0.000   ARG B1039 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.6292 (mp) cc_final: 0.5825 (tp)
REVERT: A  957 MET cc_start: 0.6236 (tpt) cc_final: 0.5818 (mmm)
REVERT: A 1076 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7155 (pp)
  outliers start: 9
  outliers final: 3
  residues processed: 60
  average time/residue: 0.1745
  time to fit residues: 15.6617
Evaluate side-chains
  51 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain B residue 1047 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0170
   chunk 52 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 92 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1001 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 = 0.4769 r_free = 0.4769 target = 0.124313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.107378 restraints weight = 40413.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.4384 rms_B_bonded: 7.07
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6128
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8044  Z= 0.124
  Angle     :  0.500   9.297  10874  Z= 0.250
  Chirality :  0.041   0.148   1160
  Planarity :  0.004   0.042   1388
  Dihedral  :  3.761  20.627   1072
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.85 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.29), residues: 950
  helix:  1.47 (0.29), residues: 382
  sheet: -0.28 (0.49), residues: 136
  loop : -1.27 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.004   0.001   HIS A1051 
 PHE   0.017   0.001   PHE B 750 
 TYR   0.021   0.001   TYR A 888 
 ARG   0.003   0.000   ARG B1039 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.6431 (mp) cc_final: 0.5940 (tp)
REVERT: A  900 ARG cc_start: 0.8253 (ptp-170) cc_final: 0.7626 (ptp-170)
REVERT: A  957 MET cc_start: 0.6217 (tpt) cc_final: 0.5787 (mmm)
  outliers start: 10
  outliers final: 2
  residues processed: 57
  average time/residue: 0.1599
  time to fit residues: 14.0129
Evaluate side-chains
  50 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue 1073 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1051 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.117420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.100621 restraints weight = 40639.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.4246 rms_B_bonded: 6.89
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
moved from start:          0.4949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8044  Z= 0.271
  Angle     :  0.648   7.959  10874  Z= 0.334
  Chirality :  0.045   0.158   1160
  Planarity :  0.005   0.053   1388
  Dihedral  :  4.798  25.149   1072
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.20 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.28), residues: 950
  helix:  0.65 (0.27), residues: 386
  sheet: -0.53 (0.49), residues: 132
  loop : -1.33 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1189 
 HIS   0.005   0.001   HIS B1078 
 PHE   0.015   0.002   PHE A 913 
 TYR   0.022   0.002   TYR A1038 
 ARG   0.006   0.001   ARG A 736 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A 1076 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7181 (pp)
REVERT: B 1073 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6182 (tt0)
  outliers start: 16
  outliers final: 9
  residues processed: 66
  average time/residue: 0.1523
  time to fit residues: 15.4173
Evaluate side-chains
  56 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  880 ASN
Chi-restraints excluded: chain A residue 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain A residue 1168 SER
Chi-restraints excluded: chain B residue  846 MET
Chi-restraints excluded: chain B residue  880 ASN
Chi-restraints excluded: chain B residue 1073 GLU
Chi-restraints excluded: chain B residue 1076 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   chunk 82 optimal weight:    0.2980
   chunk 74 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1001 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 = 0.4696 r_free = 0.4696 target = 0.120170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.103628 restraints weight = 40346.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.4310 rms_B_bonded: 6.85
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6266
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8044  Z= 0.155
  Angle     :  0.565   9.252  10874  Z= 0.283
  Chirality :  0.042   0.166   1160
  Planarity :  0.004   0.044   1388
  Dihedral  :  4.253  23.166   1072
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.03 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.28), residues: 950
  helix:  1.12 (0.28), residues: 374
  sheet: -0.01 (0.51), residues: 126
  loop : -1.48 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1170 
 HIS   0.005   0.001   HIS A1051 
 PHE   0.021   0.001   PHE A 913 
 TYR   0.011   0.001   TYR A1029 
 ARG   0.007   0.000   ARG B1087 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.6163 (mp) cc_final: 0.5593 (tp)
REVERT: A 1076 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7230 (pp)
REVERT: B 1026 ASN cc_start: 0.8367 (p0) cc_final: 0.7946 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 59
  average time/residue: 0.1605
  time to fit residues: 14.7163
Evaluate side-chains
  56 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  880 ASN
Chi-restraints excluded: chain A residue 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain A residue 1168 SER
Chi-restraints excluded: chain B residue  838 VAL
Chi-restraints excluded: chain B residue  846 MET
Chi-restraints excluded: chain B residue  957 MET
Chi-restraints excluded: chain B residue 1073 GLU
Chi-restraints excluded: chain B residue 1076 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0870
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A1001 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 = 0.4706 r_free = 0.4706 target = 0.120619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.104120 restraints weight = 40830.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 6.93
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6248
moved from start:          0.5100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8044  Z= 0.146
  Angle     :  0.544   8.363  10874  Z= 0.272
  Chirality :  0.042   0.163   1160
  Planarity :  0.004   0.043   1388
  Dihedral  :  4.083  22.028   1072
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.63 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.29), residues: 950
  helix:  1.31 (0.29), residues: 374
  sheet:  0.05 (0.51), residues: 126
  loop : -1.36 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1170 
 HIS   0.004   0.001   HIS A1051 
 PHE   0.020   0.001   PHE A 913 
 TYR   0.031   0.001   TYR A1029 
 ARG   0.003   0.000   ARG B1039 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.6164 (mp) cc_final: 0.5615 (tp)
REVERT: A 1076 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7138 (pp)
REVERT: B  775 LEU cc_start: 0.5862 (mp) cc_final: 0.5436 (tp)
REVERT: B  962 GLU cc_start: 0.7587 (tp30) cc_final: 0.7062 (tp30)
REVERT: B 1026 ASN cc_start: 0.8301 (p0) cc_final: 0.7908 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1752
  time to fit residues: 15.9879
Evaluate side-chains
  57 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  880 ASN
Chi-restraints excluded: chain A residue 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain A residue 1168 SER
Chi-restraints excluded: chain B residue  838 VAL
Chi-restraints excluded: chain B residue  957 MET
Chi-restraints excluded: chain B residue 1073 GLU
Chi-restraints excluded: chain B residue 1076 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 68 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 HIS
B 789 HIS
** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1014 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.115650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.099222 restraints weight = 41439.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 6.79
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6421
moved from start:          0.5972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8044  Z= 0.280
  Angle     :  0.679  13.322  10874  Z= 0.344
  Chirality :  0.046   0.252   1160
  Planarity :  0.005   0.064   1388
  Dihedral  :  4.845  24.926   1072
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.86 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.27), residues: 950
  helix:  0.53 (0.27), residues: 388
  sheet:  0.15 (0.54), residues: 106
  loop : -1.51 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1189 
 HIS   0.006   0.001   HIS B1078 
 PHE   0.011   0.002   PHE B 750 
 TYR   0.023   0.002   TYR A1029 
 ARG   0.005   0.001   ARG A 863 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A 1076 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7268 (pp)
REVERT: B  893 LYS cc_start: 0.9065 (mptt) cc_final: 0.8745 (mptt)
REVERT: B  962 GLU cc_start: 0.7619 (tp30) cc_final: 0.7170 (tp30)
REVERT: B 1026 ASN cc_start: 0.8359 (p0) cc_final: 0.7945 (p0)
  outliers start: 10
  outliers final: 8
  residues processed: 61
  average time/residue: 0.1717
  time to fit residues: 15.5462
Evaluate side-chains
  60 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  880 ASN
Chi-restraints excluded: chain A residue 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain A residue 1168 SER
Chi-restraints excluded: chain B residue  846 MET
Chi-restraints excluded: chain B residue  957 MET
Chi-restraints excluded: chain B residue 1076 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 52 optimal weight:    0.0050
   chunk 61 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
A1129 GLN
** B 996 GLN ** 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 = 0.4673 r_free = 0.4673 target = 0.118488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.102229 restraints weight = 40829.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.4278 rms_B_bonded: 6.84
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6293
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8044  Z= 0.168
  Angle     :  0.588  12.920  10874  Z= 0.293
  Chirality :  0.043   0.154   1160
  Planarity :  0.004   0.047   1388
  Dihedral  :  4.357  22.688   1072
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.45 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.28), residues: 950
  helix:  1.02 (0.28), residues: 374
  sheet:  0.32 (0.56), residues: 98
  loop : -1.41 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1170 
 HIS   0.009   0.001   HIS A1078 
 PHE   0.018   0.001   PHE A 913 
 TYR   0.024   0.001   TYR A1029 
 ARG   0.004   0.000   ARG B1039 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.5973 (mp) cc_final: 0.5526 (tp)
REVERT: A 1076 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7357 (pp)
REVERT: B  893 LYS cc_start: 0.9093 (mptt) cc_final: 0.8754 (mptt)
REVERT: B  962 GLU cc_start: 0.7609 (tp30) cc_final: 0.7288 (pm20)
REVERT: B 1026 ASN cc_start: 0.8275 (p0) cc_final: 0.7885 (p0)
  outliers start: 8
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1618
  time to fit residues: 15.4311
Evaluate side-chains
  61 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain A residue 1168 SER
Chi-restraints excluded: chain B residue 1076 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 92 optimal weight:    0.4980
   chunk 58 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0970
   chunk 86 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** B 996 GLN ** 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 = 0.4703 r_free = 0.4703 target = 0.119062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.103008 restraints weight = 40725.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 6.85
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6266
moved from start:          0.5997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8044  Z= 0.151
  Angle     :  0.573  12.344  10874  Z= 0.285
  Chirality :  0.043   0.154   1160
  Planarity :  0.004   0.048   1388
  Dihedral  :  4.192  20.343   1072
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 14.81 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.28), residues: 950
  helix:  1.16 (0.29), residues: 374
  sheet:  0.34 (0.57), residues: 98
  loop : -1.31 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1170 
 HIS   0.004   0.001   HIS A1078 
 PHE   0.011   0.001   PHE B 750 
 TYR   0.022   0.001   TYR A1029 
 ARG   0.004   0.000   ARG B1039 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3518.23 seconds
wall clock time: 61 minutes 29.89 seconds (3689.89 seconds total)