Starting phenix.real_space_refine
on Mon Dec 30 15:55:44 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tre_26087/12_2024/7tre_26087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tre_26087/12_2024/7tre_26087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tre_26087/12_2024/7tre_26087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tre_26087/12_2024/7tre_26087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tre_26087/12_2024/7tre_26087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tre_26087/12_2024/7tre_26087.cif"
  }
  resolution = 3.5
  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=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     P     224      5.49       5
     S      40      5.16       5
     C    7660      2.51       5
     N    2426      2.21       5
     O    3061      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 13411
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 4605
          Classifications: {'RNA': 217}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 20, 'rna3p_pur': 86, 'rna3p_pyr': 97}
          Link IDs: {'rna2p': 34, 'rna3p': 182}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 7488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 934, 7488
          Classifications: {'peptide': 934}
          Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 147
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "C"
      Number of atoms: 1171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1171
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 9, 'TRANS': 142}
  Time building chain proxies: 8.52, per 1000 atoms: 0.64
  Number of scatterers: 13411
  At special positions: 0
  Unit cell: (140.8, 122.1, 108.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P     224     15.00
     O    3061      8.00
     N    2426      7.00
     C    7660      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: 3.67
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      50.6% alpha, 14.7% beta
      61 base pairs and 96 stacking pairs defined.
    Time for finding SS restraints: 5.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 18
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 92
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.542A  pdb=" N   PHE A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 134
      removed outlier: 3.512A  pdb=" N   GLY A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.812A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 331
      No H-bonds generated for 'chain 'A' and resid 329 through 331'
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.730A  pdb=" N   ALA A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 3.943A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.828A  pdb=" N   LEU A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 453
    Processing helix  chain 'A' and resid 457 through 470
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.628A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.648A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
      removed outlier: 3.908A  pdb=" N   HIS A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
      removed outlier: 3.849A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 4.355A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS A 594 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 610
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 3.664A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.836A  pdb=" N   LEU A 676 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY A 677 " --> pdb=" O   GLY A 674 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 673 through 677'
    Processing helix  chain 'A' and resid 682 through 699
      removed outlier: 3.876A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA A 699 " --> pdb=" O   LEU A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 814
    Processing helix  chain 'A' and resid 837 through 854
    Processing helix  chain 'A' and resid 856 through 860
      removed outlier: 4.160A  pdb=" N   ASP A 860 " --> pdb=" O   ILE A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 890
      removed outlier: 3.605A  pdb=" N   GLY A 890 " --> pdb=" O   THR A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.809A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 4.033A  pdb=" N   LEU A 958 " --> pdb=" O   ARG A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 982
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
    Processing helix  chain 'A' and resid 1024 through 1027
    Processing helix  chain 'A' and resid 1028 through 1051
      removed outlier: 4.094A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1082
      removed outlier: 4.072A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TRP A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.675A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.638A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A1107 " --> pdb=" O   LEU A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1118
    Processing helix  chain 'C' and resid 98 through 104
      removed outlier: 3.865A  pdb=" N   LEU C 104 " --> pdb=" O   ARG C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 164
    Processing helix  chain 'C' and resid 167 through 171
      removed outlier: 3.507A  pdb=" N   LYS C 170 " --> pdb=" O   TRP C 167 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLU C 171 " --> pdb=" O   GLU C 168 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 167 through 171'
    Processing helix  chain 'C' and resid 223 through 226
    Processing helix  chain 'C' and resid 227 through 241
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
      removed outlier: 3.728A  pdb=" N   GLU A  20 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.962A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.973A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 20.101A  pdb=" N   SER A 797 " --> pdb=" O   CYS A 171 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   LEU A 798 " --> pdb=" O   TYR A 739 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   TYR A 739 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 600
      removed outlier: 4.566A  pdb=" N   GLN A 827 " --> pdb=" O   HIS A 816 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   HIS A 816 " --> pdb=" O   GLN A 827 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.537A  pdb=" N   VAL A 904 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ASP A 712 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   LYS A 902 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 120
      removed outlier: 7.126A  pdb=" N   LEU C 145 " --> pdb=" O   LEU C 118 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   VAL C 120 " --> pdb=" O   THR C 143 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   THR C 143 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   LEU C 204 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG C 154 " --> pdb=" O   LEU C 204 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL C 206 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU C 156 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   ARG C 208 " --> pdb=" O   LEU C 156 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ASP C 186 " --> pdb=" O   ASP C 207 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   PHE C 209 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU C 184 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU C 211 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU C 182 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ARG C 180 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG C 180 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      166 hydrogen bonds
      316 hydrogen bond angles
      0 basepair planarities
      61 basepair parallelities
      96 stacking parallelities
  Total time for adding SS restraints: 7.06

  Time building geometry restraints manager: 4.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2319
        1.33 -     1.45: 4595
        1.45 -     1.57: 6752
        1.57 -     1.69: 444
        1.69 -     1.81: 51
  Bond restraints: 14161
  Sorted by residual:
  bond pdb=" N   VAL A 127 "
       pdb=" CA  VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.41e+00
  bond pdb=" N   HIS A 609 "
       pdb=" CA  HIS A 609 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.034 1.31e-02 5.83e+03 6.84e+00
  bond pdb=" N   SER A 134 "
       pdb=" CA  SER A 134 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.22e-02 6.72e+03 6.50e+00
  bond pdb=" N   ARG A 610 "
       pdb=" CA  ARG A 610 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.32e-02 5.74e+03 6.48e+00
  bond pdb=" N   LEU A 131 "
       pdb=" CA  LEU A 131 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.030 1.21e-02 6.83e+03 6.34e+00
  ... (remaining 14156 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 19428
        1.73 -     3.47: 739
        3.47 -     5.20: 80
        5.20 -     6.93: 14
        6.93 -     8.66: 5
  Bond angle restraints: 20266
  Sorted by residual:
  angle pdb=" C4'   A B  62 "
        pdb=" C3'   A B  62 "
        pdb=" O3'   A B  62 "
      ideal   model   delta    sigma   weight residual
     113.00  107.88    5.12 1.50e+00 4.44e-01 1.17e+01
  angle pdb=" O3'   A B  55 "
        pdb=" C3'   A B  55 "
        pdb=" C2'   A B  55 "
      ideal   model   delta    sigma   weight residual
     113.70  109.21    4.49 1.50e+00 4.44e-01 8.95e+00
  angle pdb=" CA  VAL A 127 "
        pdb=" C   VAL A 127 "
        pdb=" O   VAL A 127 "
      ideal   model   delta    sigma   weight residual
     121.17  118.09    3.08 1.06e+00 8.90e-01 8.46e+00
  angle pdb=" O   GLY A 135 "
        pdb=" C   GLY A 135 "
        pdb=" N   ALA A 136 "
      ideal   model   delta    sigma   weight residual
     122.19  124.95   -2.76 9.70e-01 1.06e+00 8.10e+00
  angle pdb=" O3'   G B  71 "
        pdb=" C3'   G B  71 "
        pdb=" C2'   G B  71 "
      ideal   model   delta    sigma   weight residual
     113.70  117.95   -4.25 1.50e+00 4.44e-01 8.01e+00
  ... (remaining 20261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.50: 8136
       35.50 -    70.99: 644
       70.99 -   106.49: 95
      106.49 -   141.98: 5
      141.98 -   177.48: 3
  Dihedral angle restraints: 8883
    sinusoidal: 5729
      harmonic: 3154
  Sorted by residual:
  dihedral pdb=" O4'   U B  43 "
           pdb=" C1'   U B  43 "
           pdb=" N1    U B  43 "
           pdb=" C2    U B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   54.52  177.48     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B 133 "
           pdb=" C1'   U B 133 "
           pdb=" N1    U B 133 "
           pdb=" C2    U B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   59.89  172.11     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" O4'   U B 291 "
           pdb=" C1'   U B 291 "
           pdb=" N1    U B 291 "
           pdb=" C2    U B 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   41.00 -169.00     1      1.70e+01 3.46e-03 6.58e+01
  ... (remaining 8880 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 2011
       0.054 -    0.109: 371
       0.109 -    0.163: 62
       0.163 -    0.217: 17
       0.217 -    0.271: 8
  Chirality restraints: 2469
  Sorted by residual:
  chirality pdb=" P     G B  63 "
            pdb=" OP1   G B  63 "
            pdb=" OP2   G B  63 "
            pdb=" O5'   G B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.68   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C3'   A B  62 "
            pdb=" C4'   A B  62 "
            pdb=" O3'   A B  62 "
            pdb=" C2'   A B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.74    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" C3'   A B  55 "
            pdb=" C4'   A B  55 "
            pdb=" O3'   A B  55 "
            pdb=" C2'   A B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.72    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 2466 not shown)

  Planarity restraints: 1759
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 216 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO C 217 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 217 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 217 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 167 "    0.027 2.00e-02 2.50e+03   1.26e-02 4.35e+00
        pdb=" N9    A B 167 "   -0.030 2.00e-02 2.50e+03
        pdb=" C8    A B 167 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A B 167 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    A B 167 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A B 167 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A B 167 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A B 167 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A B 167 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A B 167 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A B 167 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 310 "    0.027 2.00e-02 2.50e+03   1.19e-02 4.23e+00
        pdb=" N9    G B 310 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8    G B 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G B 310 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G B 310 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B 310 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G B 310 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G B 310 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G B 310 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    G B 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G B 310 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1756 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1175
        2.73 -     3.27: 12061
        3.27 -     3.82: 22665
        3.82 -     4.36: 26991
        4.36 -     4.90: 41781
  Nonbonded interactions: 104673
  Sorted by model distance:
  nonbonded pdb=" O2'   A B 175 "
            pdb=" OP1   A B 176 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O   LEU A1079 "
            pdb=" OG1 THR A1083 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O2'   U B 314 "
            pdb=" OE2 GLU A 538 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O2'   A B  48 "
            pdb=" OP2   A B  49 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" N1    G B  93 "
            pdb=" O6    G B 121 "
     model   vdw
     2.253 3.120
  ... (remaining 104668 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     38.040
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  14161  Z= 0.399
  Angle     :  0.767   8.664  20266  Z= 0.418
  Chirality :  0.048   0.271   2469
  Planarity :  0.005   0.054   1759
  Dihedral  : 21.804 177.475   6839
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.64 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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: -0.75 (0.25), residues: 1074
  helix:  0.82 (0.24), residues: 477
  sheet: -1.09 (0.38), residues: 131
  loop : -1.73 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C 167 
 HIS   0.008   0.002   HIS A 592 
 PHE   0.026   0.003   PHE A 331 
 TYR   0.018   0.002   TYR A 122 
 ARG   0.009   0.001   ARG A1011 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  769 LEU cc_start: 0.7756 (pt) cc_final: 0.7495 (pt)
REVERT: A  849 MET cc_start: 0.8015 (ttp) cc_final: 0.7572 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.4467
  time to fit residues: 108.8564
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 117 optimal weight:   20.0000
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 748 GLN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14161  Z= 0.200
  Angle     :  0.610  11.249  20266  Z= 0.302
  Chirality :  0.036   0.325   2469
  Planarity :  0.005   0.050   1759
  Dihedral  : 23.080 179.773   4740
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  9.15 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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: -0.06 (0.26), residues: 1074
  helix:  1.41 (0.24), residues: 479
  sheet: -0.85 (0.38), residues: 128
  loop : -1.36 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A  60 
 HIS   0.007   0.001   HIS A 779 
 PHE   0.019   0.002   PHE A 331 
 TYR   0.011   0.001   TYR A 168 
 ARG   0.016   0.001   ARG C 113 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  849 MET cc_start: 0.7970 (ttp) cc_final: 0.7516 (ttp)
REVERT: A 1054 MET cc_start: 0.6336 (tpp) cc_final: 0.5629 (ttt)
  outliers start: 8
  outliers final: 6
  residues processed: 98
  average time/residue: 0.2763
  time to fit residues: 39.8792
Evaluate side-chains
  79 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 117 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 GLN
A 770 GLN
A 816 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14161  Z= 0.300
  Angle     :  0.631  15.231  20266  Z= 0.316
  Chirality :  0.037   0.223   2469
  Planarity :  0.005   0.045   1759
  Dihedral  : 22.927 179.508   4740
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.77 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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: -0.07 (0.26), residues: 1074
  helix:  1.36 (0.24), residues: 482
  sheet: -0.78 (0.39), residues: 123
  loop : -1.35 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  60 
 HIS   0.007   0.002   HIS A 609 
 PHE   0.024   0.002   PHE A 331 
 TYR   0.012   0.002   TYR A 176 
 ARG   0.029   0.001   ARG C 113 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  849 MET cc_start: 0.8030 (ttp) cc_final: 0.7772 (ttp)
REVERT: A 1054 MET cc_start: 0.6222 (tpp) cc_final: 0.5714 (ttt)
REVERT: C  239 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7455 (mp0)
  outliers start: 15
  outliers final: 9
  residues processed: 86
  average time/residue: 0.2666
  time to fit residues: 34.9864
Evaluate side-chains
  76 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 12 optimal weight:   10.0000
   chunk 56 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 117 optimal weight:   30.0000
   chunk 124 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN
A 794 GLN
A1051 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14161  Z= 0.165
  Angle     :  0.545  11.641  20266  Z= 0.269
  Chirality :  0.033   0.203   2469
  Planarity :  0.004   0.044   1759
  Dihedral  : 22.805 178.282   4740
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 15.21 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.39 (0.26), residues: 1074
  helix:  1.79 (0.25), residues: 480
  sheet: -0.41 (0.40), residues: 131
  loop : -1.22 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 137 
 HIS   0.003   0.001   HIS A 609 
 PHE   0.025   0.001   PHE A  47 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.004   0.000   ARG A 657 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
REVERT: A 1023 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8288 (mt0)
REVERT: A 1054 MET cc_start: 0.6357 (tpp) cc_final: 0.5864 (ttt)
REVERT: C  239 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7336 (mp0)
  outliers start: 13
  outliers final: 10
  residues processed: 87
  average time/residue: 0.2274
  time to fit residues: 30.7903
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    0.1980
   chunk 70 optimal weight:    0.5980
   chunk 1 optimal weight:   10.0000
   chunk 92 optimal weight:    0.0970
   chunk 51 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 63 optimal weight:   10.0000
   chunk 111 optimal weight:    0.2980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A 752 HIS
A 794 GLN
** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14161  Z= 0.124
  Angle     :  0.520  10.877  20266  Z= 0.255
  Chirality :  0.032   0.203   2469
  Planarity :  0.004   0.044   1759
  Dihedral  : 22.660 178.027   4740
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.17 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.56 (0.27), residues: 1074
  helix:  1.98 (0.25), residues: 483
  sheet: -0.38 (0.40), residues: 130
  loop : -1.19 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A  60 
 HIS   0.003   0.001   HIS C 151 
 PHE   0.026   0.001   PHE A  27 
 TYR   0.008   0.001   TYR A 168 
 ARG   0.004   0.000   ARG A 657 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 1.586 
Fit side-chains
   revert: symmetry clash
REVERT: A 1023 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8211 (mt0)
REVERT: A 1054 MET cc_start: 0.6308 (tpp) cc_final: 0.5946 (ttt)
  outliers start: 15
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2468
  time to fit residues: 33.9163
Evaluate side-chains
  80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 73 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:   30.0000
   chunk 65 optimal weight:    1.9990
   chunk 120 optimal weight:    7.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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: 0.7817
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14161  Z= 0.206
  Angle     :  0.546  11.428  20266  Z= 0.268
  Chirality :  0.033   0.206   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.616 177.273   4740
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 17.13 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.54 (0.27), residues: 1074
  helix:  1.89 (0.25), residues: 486
  sheet: -0.33 (0.40), residues: 131
  loop : -1.15 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 137 
 HIS   0.004   0.001   HIS C 151 
 PHE   0.023   0.002   PHE A  47 
 TYR   0.007   0.001   TYR A 462 
 ARG   0.003   0.000   ARG A 865 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 1.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1054 MET cc_start: 0.6313 (tpp) cc_final: 0.5916 (ttt)
REVERT: C  239 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7434 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 85
  average time/residue: 0.2696
  time to fit residues: 34.4003
Evaluate side-chains
  81 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 71 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 124 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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: 0.7808
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14161  Z= 0.178
  Angle     :  0.536  12.202  20266  Z= 0.262
  Chirality :  0.033   0.210   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.577 177.105   4740
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.81 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.51 (0.27), residues: 1074
  helix:  1.83 (0.25), residues: 486
  sheet: -0.30 (0.41), residues: 131
  loop : -1.13 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 137 
 HIS   0.003   0.001   HIS A 482 
 PHE   0.026   0.001   PHE A  27 
 TYR   0.008   0.001   TYR A 168 
 ARG   0.005   0.000   ARG A 132 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: A 1054 MET cc_start: 0.6319 (tpp) cc_final: 0.5932 (ttt)
REVERT: C  239 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7295 (mp0)
  outliers start: 16
  outliers final: 12
  residues processed: 87
  average time/residue: 0.2423
  time to fit residues: 32.6343
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0470
   chunk 61 optimal weight:    3.9990
   chunk 11 optimal weight:   30.0000
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0370
   chunk 119 optimal weight:   10.0000
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  14161  Z= 0.129
  Angle     :  0.513  12.066  20266  Z= 0.250
  Chirality :  0.031   0.210   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.474 177.578   4740
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 17.87 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.67 (0.27), residues: 1074
  helix:  2.01 (0.25), residues: 483
  sheet: -0.27 (0.41), residues: 131
  loop : -1.07 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 137 
 HIS   0.002   0.000   HIS A 546 
 PHE   0.027   0.001   PHE A  47 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.005   0.000   ARG A 132 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
REVERT: A 1023 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8093 (mt0)
REVERT: A 1054 MET cc_start: 0.6335 (tpp) cc_final: 0.5968 (ttt)
  outliers start: 12
  outliers final: 9
  residues processed: 84
  average time/residue: 0.2510
  time to fit residues: 32.3571
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 115 optimal weight:    8.9990
   chunk 119 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
C 190 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14161  Z= 0.177
  Angle     :  0.522  11.074  20266  Z= 0.256
  Chirality :  0.032   0.214   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 22.444 177.002   4740
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 17.34 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.63 (0.27), residues: 1074
  helix:  1.93 (0.25), residues: 486
  sheet: -0.23 (0.42), residues: 131
  loop : -1.08 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 137 
 HIS   0.002   0.001   HIS A 482 
 PHE   0.025   0.001   PHE A  47 
 TYR   0.007   0.001   TYR A 462 
 ARG   0.004   0.000   ARG A 132 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
REVERT: A 1023 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8240 (mt0)
REVERT: A 1054 MET cc_start: 0.6325 (tpp) cc_final: 0.5966 (ttt)
  outliers start: 12
  outliers final: 9
  residues processed: 79
  average time/residue: 0.2726
  time to fit residues: 32.9121
Evaluate side-chains
  79 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 128 optimal weight:    3.9990
   chunk 118 optimal weight:   20.0000
   chunk 102 optimal weight:    1.9990
   chunk 10 optimal weight:   30.0000
   chunk 79 optimal weight:    0.5980
   chunk 62 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  14161  Z= 0.161
  Angle     :  0.517  11.255  20266  Z= 0.253
  Chirality :  0.032   0.216   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 22.426 177.135   4740
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 17.45 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.63 (0.27), residues: 1074
  helix:  1.91 (0.25), residues: 486
  sheet: -0.19 (0.43), residues: 131
  loop : -1.06 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 137 
 HIS   0.002   0.001   HIS A 482 
 PHE   0.027   0.001   PHE A  47 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.004   0.000   ARG A 132 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  372 MET cc_start: 0.3841 (mmm) cc_final: 0.3250 (ttp)
REVERT: A 1054 MET cc_start: 0.6237 (tpp) cc_final: 0.5872 (ttt)
REVERT: C  168 GLU cc_start: 0.6151 (pm20) cc_final: 0.5930 (pm20)
  outliers start: 14
  outliers final: 12
  residues processed: 83
  average time/residue: 0.2257
  time to fit residues: 29.3520
Evaluate side-chains
  82 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 102 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 105 optimal weight:    0.6980
   chunk 12 optimal weight:   10.9990
   chunk 18 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 827 GLN
** C 205 GLN ** 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 = 0.4018 r_free = 0.4018 target = 0.137660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.084256 restraints weight = 27778.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.086751 restraints weight = 14967.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.088247 restraints weight = 11090.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14161  Z= 0.320
  Angle     :  0.605  10.888  20266  Z= 0.300
  Chirality :  0.036   0.222   2469
  Planarity :  0.005   0.040   1759
  Dihedral  : 22.511 177.985   4740
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 17.66 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.31 (0.26), residues: 1074
  helix:  1.55 (0.24), residues: 487
  sheet: -0.36 (0.42), residues: 137
  loop : -1.11 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP A 137 
 HIS   0.006   0.001   HIS A 482 
 PHE   0.027   0.002   PHE A 331 
 TYR   0.009   0.001   TYR A 462 
 ARG   0.003   0.000   ARG A 599 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2143.31 seconds
wall clock time: 40 minutes 27.04 seconds (2427.04 seconds total)