Starting phenix.real_space_refine
on Thu Jun 12 02:26:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tre_26087/06_2025/7tre_26087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tre_26087/06_2025/7tre_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_26087/06_2025/7tre_26087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tre_26087/06_2025/7tre_26087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tre_26087/06_2025/7tre_26087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tre_26087/06_2025/7tre_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.46, per 1000 atoms: 0.63
  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: 3.24
  Conformation dependent library (CDL) restraints added in 1.2 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: 5.45
  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: 6.90

  Time building geometry restraints manager: 3.85 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:             1.660
  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:             0.020
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     38.370
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.820
-------------------------------------------------------------------------------
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= 0.287
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12603 (  576)
  hydrogen bonds       : angle       5.11481 ( 1489)
  covalent geometry    : bond        0.00610 (14161)
  covalent geometry    : angle       0.76703 (20266)

*********************** 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  : 1.093 
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: 0.3851
  time to fit residues: 92.2820
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  : 1.071 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.144354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.091753 restraints weight = 27557.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.094469 restraints weight = 14357.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.096053 restraints weight = 10387.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
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= 0.141
  Angle     :  0.610  11.249  20266  Z= 0.302
  Chirality :  0.036   0.325   2469
  Planarity :  0.005   0.050   1759
  Dihedral  : 23.079 179.773   4740
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.27
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04764 (  576)
  hydrogen bonds       : angle       4.24404 ( 1489)
  covalent geometry    : bond        0.00309 (14161)
  covalent geometry    : angle       0.61042 (20266)

*********************** 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  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  538 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: A  849 MET cc_start: 0.8688 (ttp) cc_final: 0.8226 (ttp)
REVERT: A 1054 MET cc_start: 0.7683 (tpp) cc_final: 0.7166 (ttt)
REVERT: C  122 GLN cc_start: 0.7490 (mm-40) cc_final: 0.6985 (tt0)
  outliers start: 8
  outliers final: 6
  residues processed: 98
  average time/residue: 0.2638
  time to fit residues: 38.0382
Evaluate side-chains
  80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
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 89 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 121 optimal weight:    2.9990
   chunk 122 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:   30.0000
   chunk 70 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 30 optimal weight:    8.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 770 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.141279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.090926 restraints weight = 27728.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.091466 restraints weight = 15478.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.091699 restraints weight = 11860.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3029

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= 0.155
  Angle     :  0.577  13.579  20266  Z= 0.287
  Chirality :  0.035   0.195   2469
  Planarity :  0.005   0.047   1759
  Dihedral  : 22.859 179.441   4740
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.70 %
    Favored  : 86.91 %
  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:  0.14 (0.26), residues: 1074
  helix:  1.64 (0.24), residues: 479
  sheet: -0.77 (0.39), residues: 123
  loop : -1.31 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  60 
 HIS   0.006   0.001   HIS A 609 
 PHE   0.019   0.002   PHE A 331 
 TYR   0.011   0.001   TYR A 176 
 ARG   0.006   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04627 (  576)
  hydrogen bonds       : angle       4.05084 ( 1489)
  covalent geometry    : bond        0.00344 (14161)
  covalent geometry    : angle       0.57735 (20266)

*********************** 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
  97 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7831 (tmtt)
REVERT: A  849 MET cc_start: 0.8599 (ttp) cc_final: 0.8237 (ttp)
REVERT: A 1054 MET cc_start: 0.7456 (tpp) cc_final: 0.7065 (ttt)
REVERT: C  122 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7143 (tt0)
REVERT: C  239 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7771 (mp0)
  outliers start: 13
  outliers final: 9
  residues processed: 91
  average time/residue: 0.2378
  time to fit residues: 33.0946
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
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 C residue   94 VAL
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  183 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 107 optimal weight:    0.4980
   chunk 15 optimal weight:    9.9990
   chunk 80 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.0382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.141718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.089060 restraints weight = 27363.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.091736 restraints weight = 14261.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.093311 restraints weight = 10371.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14161  Z= 0.114
  Angle     :  0.531   9.107  20266  Z= 0.263
  Chirality :  0.033   0.202   2469
  Planarity :  0.004   0.044   1759
  Dihedral  : 22.739 178.257   4740
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.47 %
    Favored  : 84.26 %
  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:  0.40 (0.26), residues: 1074
  helix:  1.82 (0.24), residues: 481
  sheet: -0.44 (0.39), residues: 131
  loop : -1.23 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 137 
 HIS   0.005   0.001   HIS C 190 
 PHE   0.025   0.001   PHE A  47 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.007   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (  576)
  hydrogen bonds       : angle       3.86819 ( 1489)
  covalent geometry    : bond        0.00247 (14161)
  covalent geometry    : angle       0.53051 (20266)

*********************** 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
  85 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1054 MET cc_start: 0.7468 (tpp) cc_final: 0.7155 (ttt)
REVERT: C  122 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7095 (tt0)
REVERT: C  210 SER cc_start: 0.7735 (t) cc_final: 0.7064 (p)
REVERT: C  239 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7656 (mp0)
  outliers start: 12
  outliers final: 10
  residues processed: 78
  average time/residue: 0.2354
  time to fit residues: 28.9126
Evaluate side-chains
  78 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  161 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 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 89 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.1986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.140986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.091611 restraints weight = 27805.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.092148 restraints weight = 15861.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.092393 restraints weight = 12362.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3744

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= 0.122
  Angle     :  0.519   7.915  20266  Z= 0.258
  Chirality :  0.032   0.205   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.658 177.395   4740
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.89 %
    Favored  : 83.72 %
  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:  0.55 (0.27), residues: 1074
  helix:  1.90 (0.25), residues: 486
  sheet: -0.28 (0.40), residues: 130
  loop : -1.16 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A  60 
 HIS   0.003   0.001   HIS C 151 
 PHE   0.027   0.002   PHE A  27 
 TYR   0.008   0.001   TYR A 168 
 ARG   0.007   0.000   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (  576)
  hydrogen bonds       : angle       3.75591 ( 1489)
  covalent geometry    : bond        0.00268 (14161)
  covalent geometry    : angle       0.51944 (20266)

*********************** 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
  87 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  970 MET cc_start: 0.9290 (ttm) cc_final: 0.9075 (ttt)
REVERT: A 1023 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8427 (mt0)
REVERT: C  122 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7231 (tt0)
  outliers start: 13
  outliers final: 8
  residues processed: 81
  average time/residue: 0.2351
  time to fit residues: 29.2363
Evaluate side-chains
  74 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:   30.0000
   chunk 12 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0570
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.8700

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

Flipped N/Q/H residues before XYZ refinement:
A 752 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.142021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.092799 restraints weight = 27859.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.093393 restraints weight = 15994.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.093696 restraints weight = 12232.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  14161  Z= 0.104
  Angle     :  0.508  10.078  20266  Z= 0.249
  Chirality :  0.032   0.207   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.601 177.440   4740
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.89 %
    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:  0.62 (0.27), residues: 1074
  helix:  2.01 (0.25), residues: 483
  sheet: -0.31 (0.40), residues: 131
  loop : -1.14 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 137 
 HIS   0.002   0.001   HIS A 609 
 PHE   0.023   0.001   PHE A  47 
 TYR   0.008   0.001   TYR A 168 
 ARG   0.003   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  576)
  hydrogen bonds       : angle       3.71501 ( 1489)
  covalent geometry    : bond        0.00228 (14161)
  covalent geometry    : angle       0.50795 (20266)

*********************** 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
  90 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 1.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1023 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8375 (mt0)
REVERT: C  122 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7241 (tt0)
REVERT: C  239 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7644 (mp0)
  outliers start: 16
  outliers final: 10
  residues processed: 83
  average time/residue: 0.2394
  time to fit residues: 30.7471
Evaluate side-chains
  78 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
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  120 VAL
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:   10.9990
   chunk 128 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 117 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 3 optimal weight:   30.0000
   chunk 121 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 384 GLN
** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 827 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.137857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.087957 restraints weight = 27808.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.087839 restraints weight = 16049.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.088057 restraints weight = 13014.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14161  Z= 0.237
  Angle     :  0.624  10.438  20266  Z= 0.309
  Chirality :  0.037   0.214   2469
  Planarity :  0.005   0.074   1759
  Dihedral  : 22.647 177.701   4740
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.21 %
    Favored  : 82.98 %
  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:  0.26 (0.26), residues: 1074
  helix:  1.54 (0.24), residues: 485
  sheet: -0.36 (0.42), residues: 131
  loop : -1.16 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 137 
 HIS   0.005   0.001   HIS A 816 
 PHE   0.028   0.002   PHE A 331 
 TYR   0.011   0.001   TYR A1089 
 ARG   0.005   0.001   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05403 (  576)
  hydrogen bonds       : angle       4.08174 ( 1489)
  covalent geometry    : bond        0.00533 (14161)
  covalent geometry    : angle       0.62387 (20266)

*********************** 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
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A 1023 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8436 (mt0)
  outliers start: 17
  outliers final: 13
  residues processed: 80
  average time/residue: 0.2133
  time to fit residues: 27.0712
Evaluate side-chains
  76 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
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  161 LEU
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  827 GLN
Chi-restraints excluded: chain A residue  997 VAL
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
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 101 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0370
   chunk 47 optimal weight:    2.9990
   chunk 3 optimal weight:   30.0000
   chunk 75 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0770
   chunk 119 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
A 775 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.141034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.091000 restraints weight = 27805.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.091732 restraints weight = 16208.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.092075 restraints weight = 12109.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14161  Z= 0.100
  Angle     :  0.530  11.244  20266  Z= 0.260
  Chirality :  0.032   0.213   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 22.593 177.419   4740
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  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:  1.85 (0.25), residues: 484
  sheet: -0.22 (0.42), residues: 131
  loop : -1.08 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 137 
 HIS   0.003   0.001   HIS C 151 
 PHE   0.027   0.001   PHE A  47 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.005   0.000   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  576)
  hydrogen bonds       : angle       3.77734 ( 1489)
  covalent geometry    : bond        0.00212 (14161)
  covalent geometry    : angle       0.52968 (20266)

*********************** 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
  84 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 1.162 
Fit side-chains
REVERT: A 1023 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8279 (mt0)
REVERT: C  122 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7359 (tt0)
REVERT: C  168 GLU cc_start: 0.7583 (pm20) cc_final: 0.7315 (pm20)
  outliers start: 15
  outliers final: 10
  residues processed: 79
  average time/residue: 0.2230
  time to fit residues: 28.5422
Evaluate side-chains
  78 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
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  709 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
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
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 118 optimal weight:   30.0000
   chunk 19 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.140794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.091138 restraints weight = 27529.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.091968 restraints weight = 17315.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.092810 restraints weight = 11856.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14161  Z= 0.109
  Angle     :  0.523  10.587  20266  Z= 0.257
  Chirality :  0.032   0.212   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 22.495 177.080   4740
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 16.49 %
    Favored  : 82.13 %
  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:  0.64 (0.27), residues: 1074
  helix:  1.96 (0.25), residues: 483
  sheet: -0.26 (0.42), residues: 131
  loop : -1.07 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 137 
 HIS   0.003   0.001   HIS C 151 
 PHE   0.025   0.001   PHE A  47 
 TYR   0.006   0.001   TYR A 168 
 ARG   0.005   0.000   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  576)
  hydrogen bonds       : angle       3.73200 ( 1489)
  covalent geometry    : bond        0.00239 (14161)
  covalent geometry    : angle       0.52340 (20266)

*********************** 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
  84 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.287 
Fit side-chains
REVERT: A 1023 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8370 (mt0)
REVERT: C  122 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7275 (tt0)
REVERT: C  168 GLU cc_start: 0.7552 (pm20) cc_final: 0.7321 (pm20)
  outliers start: 13
  outliers final: 12
  residues processed: 80
  average time/residue: 0.2512
  time to fit residues: 32.3752
Evaluate side-chains
  80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
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  161 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 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  120 VAL
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 67 optimal weight:    0.7980
   chunk 9 optimal weight:   20.0000
   chunk 42 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0020
   chunk 122 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0870
   chunk 6 optimal weight:    7.9990
   overall best weight:    0.5566

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

Flipped N/Q/H residues before XYZ refinement:
A 687 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.142479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.093209 restraints weight = 27664.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.093758 restraints weight = 16208.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.094169 restraints weight = 12133.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14161  Z= 0.094
  Angle     :  0.512  10.432  20266  Z= 0.249
  Chirality :  0.032   0.214   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.431 177.497   4740
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.91 %
    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:  0.73 (0.27), residues: 1074
  helix:  2.04 (0.25), residues: 483
  sheet: -0.24 (0.42), residues: 131
  loop : -1.01 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 137 
 HIS   0.003   0.001   HIS C 151 
 PHE   0.027   0.001   PHE A  47 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.004   0.000   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  576)
  hydrogen bonds       : angle       3.66697 ( 1489)
  covalent geometry    : bond        0.00203 (14161)
  covalent geometry    : angle       0.51189 (20266)

********************** 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
  87 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 1.099 
Fit side-chains
REVERT: A 1023 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8258 (mt0)
REVERT: A 1054 MET cc_start: 0.6952 (ttt) cc_final: 0.6676 (ttt)
REVERT: C  122 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7274 (tt0)
REVERT: C  168 GLU cc_start: 0.7506 (pm20) cc_final: 0.7250 (pm20)
  outliers start: 14
  outliers final: 11
  residues processed: 83
  average time/residue: 0.2325
  time to fit residues: 29.8924
Evaluate side-chains
  80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
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  161 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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 6 optimal weight:   10.0000
   chunk 124 optimal weight:   30.0000
   chunk 90 optimal weight:    0.1980
   chunk 114 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9980
   chunk 0 optimal weight:   30.0000
   chunk 103 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0070
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.141810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.089238 restraints weight = 27747.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.091884 restraints weight = 14615.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.093477 restraints weight = 10613.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14161  Z= 0.100
  Angle     :  0.515  11.196  20266  Z= 0.250
  Chirality :  0.032   0.214   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.395 177.078   4740
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  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:  0.74 (0.27), residues: 1074
  helix:  2.06 (0.25), residues: 483
  sheet: -0.13 (0.43), residues: 129
  loop : -1.05 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A 137 
 HIS   0.011   0.001   HIS C 151 
 PHE   0.026   0.001   PHE A  47 
 TYR   0.007   0.001   TYR A 168 
 ARG   0.004   0.000   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  576)
  hydrogen bonds       : angle       3.68325 ( 1489)
  covalent geometry    : bond        0.00218 (14161)
  covalent geometry    : angle       0.51525 (20266)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3916.61 seconds
wall clock time: 69 minutes 1.57 seconds (4141.57 seconds total)