Starting phenix.real_space_refine
on Sat Dec 28 06:59:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j88_36063/12_2024/8j88_36063.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j88_36063/12_2024/8j88_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_36063/12_2024/8j88_36063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j88_36063/12_2024/8j88_36063.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j88_36063/12_2024/8j88_36063.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j88_36063/12_2024/8j88_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-5532/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: 7.96, per 1000 atoms: 1.01
  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: 1.89
  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: 0.82
  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: 2.05

  Time building geometry restraints manager: 2.18 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             6.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     23.340
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.960
-------------------------------------------------------------------------------
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  : 0.841 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1952
  time to fit residues: 19.8130
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  : 0.872 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5956
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  : 0.883 
Fit side-chains
REVERT: B  903 ASN cc_start: 0.8013 (m-40) cc_final: 0.7751 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 62
  average time/residue: 0.1718
  time to fit residues: 15.8439
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  : 0.851 
-------------------------------------------------------------------------------
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 47 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0070
   chunk 76 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.8800

-------------------------------------------------------------------------------
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**
** B1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5988
moved from start:          0.2969

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= 0.158
  Angle     :  0.524   8.735  10874  Z= 0.268
  Chirality :  0.042   0.134   1160
  Planarity :  0.004   0.040   1388
  Dihedral  :  4.062  21.137   1072
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.60 %
    Favored  : 89.81 %
  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: -0.23 (0.28), residues: 950
  helix:  1.15 (0.28), residues: 380
  sheet: -0.57 (0.52), residues: 122
  loop : -1.17 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 856 
 HIS   0.005   0.001   HIS A1051 
 PHE   0.018   0.001   PHE B 913 
 TYR   0.010   0.001   TYR B 769 
 ARG   0.003   0.000   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
  59 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.6256 (mp) cc_final: 0.5969 (tp)
REVERT: A  957 MET cc_start: 0.6204 (tpt) cc_final: 0.5828 (mmm)
REVERT: B  957 MET cc_start: 0.6535 (tpt) cc_final: 0.6026 (mmm)
REVERT: B 1026 ASN cc_start: 0.8012 (p0) cc_final: 0.7719 (p0)
  outliers start: 5
  outliers final: 3
  residues processed: 57
  average time/residue: 0.1589
  time to fit residues: 14.0812
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  : 0.959 
-------------------------------------------------------------------------------
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 84 optimal weight:    0.0010
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    0.7386

-------------------------------------------------------------------------------
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**
B 753 HIS
** B1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6003
moved from start:          0.3440

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= 0.148
  Angle     :  0.507   8.245  10874  Z= 0.259
  Chirality :  0.041   0.131   1160
  Planarity :  0.004   0.042   1388
  Dihedral  :  4.005  22.052   1072
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.02 %
    Favored  : 87.91 %
  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: -0.12 (0.28), residues: 950
  helix:  1.36 (0.28), residues: 380
  sheet: -0.55 (0.50), residues: 128
  loop : -1.23 (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   0.025   0.001   PHE B 750 
 TYR   0.014   0.001   TYR A 769 
 ARG   0.002   0.000   ARG B1087 

*********************** 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
  60 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A  957 MET cc_start: 0.6244 (tpt) cc_final: 0.5794 (mmm)
REVERT: A 1076 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7051 (pp)
  outliers start: 9
  outliers final: 1
  residues processed: 59
  average time/residue: 0.2042
  time to fit residues: 17.2300
Evaluate side-chains
  48 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue 1076 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 0 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6066
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8044  Z= 0.160
  Angle     :  0.527   8.395  10874  Z= 0.268
  Chirality :  0.042   0.154   1160
  Planarity :  0.004   0.042   1388
  Dihedral  :  4.041  22.092   1072
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.02 %
    Favored  : 86.73 %
  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:  1.29 (0.29), residues: 374
  sheet: -0.28 (0.49), residues: 136
  loop : -1.33 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1189 
 HIS   0.005   0.001   HIS A1051 
 PHE   0.017   0.001   PHE B 750 
 TYR   0.024   0.002   TYR A 888 
 ARG   0.005   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
  70 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 51
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A  775 LEU cc_start: 0.6177 (mp) cc_final: 0.5862 (tp)
REVERT: A  957 MET cc_start: 0.6300 (tpt) cc_final: 0.5894 (tpt)
  outliers start: 19
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1781
  time to fit residues: 17.0636
Evaluate side-chains
  56 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6163
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8044  Z= 0.201
  Angle     :  0.580   9.443  10874  Z= 0.293
  Chirality :  0.042   0.149   1160
  Planarity :  0.004   0.042   1388
  Dihedral  :  4.373  23.727   1072
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.49 %
    Favored  : 86.49 %
  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: -0.43 (0.28), residues: 950
  helix:  0.92 (0.28), residues: 388
  sheet: -0.35 (0.48), residues: 136
  loop : -1.39 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1189 
 HIS   0.005   0.001   HIS A1051 
 PHE   0.020   0.001   PHE A 913 
 TYR   0.015   0.002   TYR A1038 
 ARG   0.004   0.000   ARG B 900 

*********************** 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
  73 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A 1076 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7095 (pp)
REVERT: B 1073 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6420 (tt0)
  outliers start: 17
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1563
  time to fit residues: 16.8118
Evaluate side-chains
  59 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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 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 1070 GLU
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 10 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 41 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0040
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6194

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6092
moved from start:          0.4902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8044  Z= 0.149
  Angle     :  0.558   8.776  10874  Z= 0.278
  Chirality :  0.042   0.170   1160
  Planarity :  0.004   0.044   1388
  Dihedral  :  4.124  21.703   1072
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.15 %
    Favored  : 85.43 %
  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: -0.28 (0.28), residues: 950
  helix:  1.21 (0.28), residues: 376
  sheet: -0.30 (0.49), residues: 136
  loop : -1.41 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.005   0.001   HIS B1051 
 PHE   0.024   0.001   PHE B 913 
 TYR   0.009   0.001   TYR A1029 
 ARG   0.008   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
  64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 1.242 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.5850 (mp) cc_final: 0.5471 (tp)
REVERT: A 1076 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7000 (pp)
REVERT: B 1026 ASN cc_start: 0.8147 (p0) cc_final: 0.7753 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1549
  time to fit residues: 14.6531
Evaluate side-chains
  59 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
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 27 optimal weight:    0.1980
   chunk 17 optimal weight:    0.2980
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 8 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6035
moved from start:          0.5015

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= 0.134
  Angle     :  0.548  10.605  10874  Z= 0.270
  Chirality :  0.041   0.147   1160
  Planarity :  0.004   0.044   1388
  Dihedral  :  3.928  19.121   1072
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.98 %
    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:  0.02 (0.29), residues: 950
  helix:  1.36 (0.29), residues: 378
  sheet:  0.34 (0.54), residues: 114
  loop : -1.27 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1170 
 HIS   0.004   0.001   HIS B1051 
 PHE   0.023   0.001   PHE B 913 
 TYR   0.017   0.001   TYR B1029 
 ARG   0.002   0.000   ARG A1066 

*********************** 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
  67 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.5820 (mp) cc_final: 0.5594 (tp)
REVERT: A 1073 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5607 (tt0)
REVERT: A 1076 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6937 (pp)
REVERT: B  775 LEU cc_start: 0.5830 (mp) cc_final: 0.5376 (tp)
REVERT: B  893 LYS cc_start: 0.8922 (mptt) cc_final: 0.8576 (mptt)
REVERT: B  962 GLU cc_start: 0.7569 (tp30) cc_final: 0.7023 (tp30)
REVERT: B 1026 ASN cc_start: 0.8075 (p0) cc_final: 0.7874 (p0)
REVERT: B 1073 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6124 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.1701
  time to fit residues: 16.7068
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  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
Chi-restraints excluded: chain B residue  838 VAL
Chi-restraints excluded: chain B residue  846 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 86 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6122
moved from start:          0.5342

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= 0.169
  Angle     :  0.573   9.678  10874  Z= 0.286
  Chirality :  0.042   0.161   1160
  Planarity :  0.004   0.046   1388
  Dihedral  :  4.121  20.397   1072
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.98 %
    Favored  : 84.72 %
  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: -0.16 (0.29), residues: 950
  helix:  1.30 (0.29), residues: 376
  sheet:  0.05 (0.51), residues: 126
  loop : -1.42 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1189 
 HIS   0.005   0.001   HIS B1051 
 PHE   0.011   0.001   PHE B 750 
 TYR   0.035   0.002   TYR A 769 
 ARG   0.003   0.000   ARG B1087 

*********************** 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
  71 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.5963 (mp) cc_final: 0.5479 (tp)
REVERT: A 1073 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.5672 (tt0)
REVERT: A 1076 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7144 (pp)
REVERT: B  893 LYS cc_start: 0.8969 (mptt) cc_final: 0.8654 (mptt)
REVERT: B  962 GLU cc_start: 0.7598 (tp30) cc_final: 0.7258 (pm20)
REVERT: B 1026 ASN cc_start: 0.8059 (p0) cc_final: 0.7857 (p0)
REVERT: B 1073 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6122 (tt0)
  outliers start: 11
  outliers final: 7
  residues processed: 69
  average time/residue: 0.1798
  time to fit residues: 18.4551
Evaluate side-chains
  65 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  838 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   chunk 86 optimal weight:    0.8980
   chunk 74 optimal weight:    0.3980
   chunk 7 optimal weight:    0.3980
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6093
moved from start:          0.5557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8044  Z= 0.154
  Angle     :  0.564   9.230  10874  Z= 0.280
  Chirality :  0.042   0.151   1160
  Planarity :  0.004   0.046   1388
  Dihedral  :  4.033  19.719   1072
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 14.22 %
    Favored  : 84.72 %
  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: -0.08 (0.29), residues: 950
  helix:  1.26 (0.29), residues: 378
  sheet:  0.32 (0.54), residues: 114
  loop : -1.31 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1189 
 HIS   0.004   0.001   HIS B1051 
 PHE   0.019   0.001   PHE A 913 
 TYR   0.022   0.001   TYR B1029 
 ARG   0.002   0.000   ARG A1039 

********************** 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
  64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A  775 LEU cc_start: 0.6013 (mp) cc_final: 0.5650 (tp)
REVERT: A 1073 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5686 (tt0)
REVERT: A 1076 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7092 (pp)
REVERT: B  775 LEU cc_start: 0.5857 (mp) cc_final: 0.5387 (tp)
REVERT: B  893 LYS cc_start: 0.8990 (mptt) cc_final: 0.8682 (mptt)
REVERT: B  962 GLU cc_start: 0.7564 (tp30) cc_final: 0.7241 (pm20)
REVERT: B 1073 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6027 (tt0)
  outliers start: 9
  outliers final: 6
  residues processed: 62
  average time/residue: 0.1602
  time to fit residues: 15.2399
Evaluate side-chains
  62 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue 1073 GLU
Chi-restraints excluded: chain A residue 1076 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0070
   chunk 20 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
A1129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.119848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.103658 restraints weight = 40540.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.4314 rms_B_bonded: 6.83
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
moved from start:          0.5739

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= 0.154
  Angle     :  0.562   8.788  10874  Z= 0.280
  Chirality :  0.042   0.144   1160
  Planarity :  0.004   0.049   1388
  Dihedral  :  4.019  19.300   1072
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 14.57 %
    Favored  : 84.36 %
  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: -0.02 (0.29), residues: 950
  helix:  1.35 (0.29), residues: 374
  sheet:  0.33 (0.54), residues: 114
  loop : -1.30 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.004   0.001   HIS B1051 
 PHE   0.016   0.001   PHE B1164 
 TYR   0.020   0.001   TYR B1029 
 ARG   0.002   0.000   ARG A1039 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1873.81 seconds
wall clock time: 35 minutes 4.41 seconds (2104.41 seconds total)