Starting phenix.real_space_refine
on Thu Sep 26 07:01:37 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/09_2024/7trd_26086.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/09_2024/7trd_26086.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/09_2024/7trd_26086.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/09_2024/7trd_26086.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/09_2024/7trd_26086.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/09_2024/7trd_26086.cif"
  }
  resolution = 3.3
  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=   0.003
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      36      5.16       5
     C    6931      2.51       5
     N    2219      2.21       5
     O    2830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 12240
  Number of models: 1
  Model: ""
    Number of chains: 3
    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': 21, 'rna3p_pur': 86, 'rna3p_pyr': 96}
          Link IDs: {'rna2p': 35, 'rna3p': 181}
          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: "N"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 147
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
  Time building chain proxies: 7.93, per 1000 atoms: 0.65
  Number of scatterers: 12240
  At special positions: 0
  Unit cell: (108.9, 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      36     16.00
     P     224     15.00
     O    2830      8.00
     N    2219      7.00
     C    6931      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: 3.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      55.4% alpha, 15.2% beta
      64 base pairs and 96 stacking pairs defined.
    Time for finding SS restraints: 4.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 18
      removed outlier: 3.604A  pdb=" N   ARG A  11 " --> pdb=" O   CYS A   7 " (cutoff:3.500A)
    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 125 through 134
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 146 through 156
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.839A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
      removed outlier: 3.999A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 332'
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.574A  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 401
      removed outlier: 4.037A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.782A  pdb=" N   LEU A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 454
      removed outlier: 3.781A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 471
      removed outlier: 3.716A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.506A  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: 3.655A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 560
      removed outlier: 3.764A  pdb=" N   HIS A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   VAL A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 4.387A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.515A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 3.531A  pdb=" N   SER A 656 " --> pdb=" O   GLU A 652 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.651A  pdb=" N   LEU A 676 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.762A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 4.006A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.582A  pdb=" N   PHE A 776 " --> pdb=" O   TYR A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 837 through 854
    Processing helix  chain 'A' and resid 876 through 890
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.789A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 4.052A  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: 4.120A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1082
      removed outlier: 4.323A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TRP A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.651A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.508A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1119
      removed outlier: 3.712A  pdb=" N   ALA A1119 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600
      removed outlier: 6.601A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.640A  pdb=" N   VAL A 904 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASP A 712 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LYS A 902 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930

    396 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      174 hydrogen bonds
      332 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      96 stacking parallelities
  Total time for adding SS restraints: 6.92

  Time building geometry restraints manager: 3.83 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: 2612
        1.33 -     1.45: 3958
        1.45 -     1.57: 5907
        1.57 -     1.69: 444
        1.69 -     1.81: 47
  Bond restraints: 12968
  Sorted by residual:
  bond pdb=" C   LYS A 973 "
       pdb=" N   LEU A 974 "
    ideal  model  delta    sigma   weight residual
    1.334  1.384 -0.049 1.27e-02 6.20e+03 1.50e+01
  bond pdb=" N   VAL A 697 "
       pdb=" CA  VAL A 697 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.11e+00
  bond pdb=" N   VAL A 127 "
       pdb=" CA  VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.97e+00
  bond pdb=" N   ASN A 125 "
       pdb=" CA  ASN A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.031 1.22e-02 6.72e+03 6.26e+00
  bond pdb=" N   GLU A 705 "
       pdb=" CA  GLU A 705 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.28e-02 6.10e+03 6.06e+00
  ... (remaining 12963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 17958
        1.52 -     3.05: 595
        3.05 -     4.57: 76
        4.57 -     6.09: 14
        6.09 -     7.61: 1
  Bond angle restraints: 18644
  Sorted by residual:
  angle pdb=" O   LYS A 973 "
        pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
      ideal   model   delta    sigma   weight residual
     122.07  117.19    4.88 1.03e+00 9.43e-01 2.25e+01
  angle pdb=" N   VAL A 596 "
        pdb=" CA  VAL A 596 "
        pdb=" C   VAL A 596 "
      ideal   model   delta    sigma   weight residual
     112.43  108.61    3.82 9.20e-01 1.18e+00 1.73e+01
  angle pdb=" CA  LYS A 973 "
        pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
      ideal   model   delta    sigma   weight residual
     117.07  121.64   -4.57 1.14e+00 7.69e-01 1.61e+01
  angle pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
        pdb=" CA  LEU A 974 "
      ideal   model   delta    sigma   weight residual
     120.44  125.62   -5.18 1.30e+00 5.92e-01 1.59e+01
  angle pdb=" N   ASP A1038 "
        pdb=" CA  ASP A1038 "
        pdb=" C   ASP A1038 "
      ideal   model   delta    sigma   weight residual
     113.28  109.10    4.18 1.22e+00 6.72e-01 1.18e+01
  ... (remaining 18639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.85: 7444
       35.85 -    71.70: 614
       71.70 -   107.56: 96
      107.56 -   143.41: 4
      143.41 -   179.26: 3
  Dihedral angle restraints: 8161
    sinusoidal: 5438
      harmonic: 2723
  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   52.74  179.26     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
    -128.00   48.74 -176.74     1      1.70e+01 3.46e-03 6.64e+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   40.41 -168.41     1      1.70e+01 3.46e-03 6.58e+01
  ... (remaining 8158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1913
       0.048 -    0.095: 287
       0.095 -    0.143: 61
       0.143 -    0.190: 22
       0.190 -    0.238: 2
  Chirality restraints: 2285
  Sorted by residual:
  chirality pdb=" P     G B 130 "
            pdb=" OP1   G B 130 "
            pdb=" OP2   G B 130 "
            pdb=" O5'   G B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.65   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C1'   A B 174 "
            pdb=" O4'   A B 174 "
            pdb=" C2'   A B 174 "
            pdb=" N9    A B 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.24    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" C3'   G B 130 "
            pdb=" C4'   G B 130 "
            pdb=" O3'   G B 130 "
            pdb=" C2'   G B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.67    0.19 2.00e-01 2.50e+01 8.80e-01
  ... (remaining 2282 not shown)

  Planarity restraints: 1542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 130 "   -0.001 2.00e-02 2.50e+03   4.15e-02 5.17e+01
        pdb=" N9    G B 130 "    0.002 2.00e-02 2.50e+03
        pdb=" C8    G B 130 "   -0.010 2.00e-02 2.50e+03
        pdb=" N7    G B 130 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B 130 "    0.036 2.00e-02 2.50e+03
        pdb=" C6    G B 130 "   -0.105 2.00e-02 2.50e+03
        pdb=" O6    G B 130 "    0.069 2.00e-02 2.50e+03
        pdb=" N1    G B 130 "   -0.039 2.00e-02 2.50e+03
        pdb=" C2    G B 130 "    0.046 2.00e-02 2.50e+03
        pdb=" N2    G B 130 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    G B 130 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G B 130 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 129 "    0.003 2.00e-02 2.50e+03   3.20e-02 2.82e+01
        pdb=" N9    A B 129 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8    A B 129 "   -0.008 2.00e-02 2.50e+03
        pdb=" N7    A B 129 "   -0.015 2.00e-02 2.50e+03
        pdb=" C5    A B 129 "    0.075 2.00e-02 2.50e+03
        pdb=" C6    A B 129 "    0.020 2.00e-02 2.50e+03
        pdb=" N6    A B 129 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1    A B 129 "   -0.045 2.00e-02 2.50e+03
        pdb=" C2    A B 129 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    A B 129 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A B 129 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 131 "   -0.015 2.00e-02 2.50e+03   3.41e-02 2.62e+01
        pdb=" N1    C B 131 "   -0.012 2.00e-02 2.50e+03
        pdb=" C2    C B 131 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C B 131 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    C B 131 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    C B 131 "    0.077 2.00e-02 2.50e+03
        pdb=" N4    C B 131 "   -0.064 2.00e-02 2.50e+03
        pdb=" C5    C B 131 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    C B 131 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1539 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1470
        2.74 -     3.28: 11066
        3.28 -     3.82: 21444
        3.82 -     4.36: 24209
        4.36 -     4.90: 37863
  Nonbonded interactions: 96052
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1079 "
            pdb=" OG1 THR A1083 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O2'   G B  71 "
            pdb=" OP1   C B  72 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER A 619 "
            pdb=" O   ASN A 635 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O2'   A B 175 "
            pdb=" OP1   A B 176 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O2'   U B 314 "
            pdb=" OE2 GLU A 538 "
     model   vdw
     2.293 3.040
  ... (remaining 96047 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  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:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     35.900
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
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      :  0.004   0.049  12968  Z= 0.243
  Angle     :  0.636   7.614  18644  Z= 0.378
  Chirality :  0.039   0.238   2285
  Planarity :  0.005   0.042   1542
  Dihedral  : 21.934 179.261   6395
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.86 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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: -0.10 (0.28), residues: 924
  helix:  1.00 (0.26), residues: 443
  sheet: -0.29 (0.51), residues: 93
  loop : -1.25 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 581 
 HIS   0.011   0.001   HIS A 779 
 PHE   0.026   0.002   PHE A1021 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.006   0.001   ARG A 470 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4197 (mmp) cc_final: 0.3919 (mmm)
REVERT: A  700 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7503 (mt0)
REVERT: A 1059 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8219 (ttmm)
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 0.3773
  time to fit residues: 24.8805
Evaluate side-chains
  33 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  700 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    0.2980
   chunk 66 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 779 HIS
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1023 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12968  Z= 0.191
  Angle     :  0.574   8.638  18644  Z= 0.289
  Chirality :  0.034   0.174   2285
  Planarity :  0.005   0.037   1542
  Dihedral  : 23.394 179.923   4579
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.67 %
    Favored  : 93.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.29), residues: 924
  helix:  1.34 (0.25), residues: 452
  sheet: -0.18 (0.48), residues: 103
  loop : -1.06 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 581 
 HIS   0.008   0.001   HIS A 779 
 PHE   0.016   0.001   PHE A1021 
 TYR   0.009   0.001   TYR A1044 
 ARG   0.007   0.000   ARG A  83 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A 1059 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8172 (ttmm)
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.2185
  time to fit residues: 14.8237
Evaluate side-chains
  37 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    0.4980
   chunk 32 optimal weight:   10.0000
   chunk 86 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 102 optimal weight:    0.0170
   chunk 35 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12968  Z= 0.131
  Angle     :  0.515   8.210  18644  Z= 0.259
  Chirality :  0.032   0.186   2285
  Planarity :  0.004   0.035   1542
  Dihedral  : 23.273 178.905   4576
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  8.00 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.29), residues: 924
  helix:  1.64 (0.25), residues: 454
  sheet:  0.01 (0.49), residues: 96
  loop : -0.88 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 581 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.010   0.001   PHE A 331 
 TYR   0.021   0.001   TYR A 168 
 ARG   0.005   0.000   ARG A 132 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A  536 LEU cc_start: 0.8985 (tp) cc_final: 0.8661 (tp)
REVERT: A  962 ARG cc_start: 0.8641 (pmt170) cc_final: 0.7314 (pmt170)
REVERT: A 1059 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8161 (ttmm)
  outliers start: 2
  outliers final: 1
  residues processed: 41
  average time/residue: 0.2286
  time to fit residues: 14.8582
Evaluate side-chains
  39 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  779 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 11 optimal weight:   30.0000
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 110 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12968  Z= 0.196
  Angle     :  0.530   8.543  18644  Z= 0.266
  Chirality :  0.032   0.185   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 23.205 178.282   4576
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.24 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.80 (0.29), residues: 924
  helix:  1.72 (0.25), residues: 455
  sheet:  0.11 (0.50), residues: 96
  loop : -0.85 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 581 
 HIS   0.007   0.001   HIS A 779 
 PHE   0.017   0.001   PHE A 331 
 TYR   0.015   0.001   TYR A 168 
 ARG   0.009   0.000   ARG A 132 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A 1059 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8169 (ttmm)
  outliers start: 7
  outliers final: 5
  residues processed: 42
  average time/residue: 0.2220
  time to fit residues: 14.8344
Evaluate side-chains
  40 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 56 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0670
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12968  Z= 0.130
  Angle     :  0.503   8.737  18644  Z= 0.252
  Chirality :  0.031   0.189   2285
  Planarity :  0.004   0.047   1542
  Dihedral  : 23.150 178.059   4576
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 11.21 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.94 (0.29), residues: 924
  helix:  1.87 (0.25), residues: 455
  sheet:  0.17 (0.50), residues: 96
  loop : -0.83 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 581 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.011   0.001   PHE A 331 
 TYR   0.013   0.001   TYR A 168 
 ARG   0.008   0.000   ARG A 132 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 1.090 
Fit side-chains
REVERT: A 1059 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8177 (ttmm)
  outliers start: 5
  outliers final: 2
  residues processed: 41
  average time/residue: 0.2112
  time to fit residues: 14.5655
Evaluate side-chains
  41 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 99 optimal weight:    0.3980
   chunk 21 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9980
   chunk 9 optimal weight:   20.0000
   chunk 36 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12968  Z= 0.123
  Angle     :  0.492   8.808  18644  Z= 0.246
  Chirality :  0.030   0.192   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 23.083 177.822   4576
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.33 %
    Favored  : 87.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.06 (0.29), residues: 924
  helix:  1.99 (0.25), residues: 455
  sheet:  0.35 (0.54), residues: 86
  loop : -0.81 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 581 
 HIS   0.012   0.001   HIS A 779 
 PHE   0.011   0.001   PHE A 331 
 TYR   0.012   0.001   TYR A 168 
 ARG   0.006   0.000   ARG A 132 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A  536 LEU cc_start: 0.8945 (tp) cc_final: 0.8598 (tp)
REVERT: A 1059 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8285 (ttmt)
  outliers start: 6
  outliers final: 5
  residues processed: 45
  average time/residue: 0.2140
  time to fit residues: 15.9623
Evaluate side-chains
  43 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0060
   chunk 80 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12968  Z= 0.132
  Angle     :  0.492   8.816  18644  Z= 0.245
  Chirality :  0.031   0.194   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 23.036 177.585   4576
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 12.19 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.11 (0.29), residues: 924
  helix:  2.03 (0.25), residues: 457
  sheet:  0.33 (0.54), residues: 86
  loop : -0.79 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 581 
 HIS   0.004   0.001   HIS A 609 
 PHE   0.012   0.001   PHE A 331 
 TYR   0.011   0.001   TYR A 168 
 ARG   0.006   0.000   ARG A 132 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A  536 LEU cc_start: 0.8952 (tp) cc_final: 0.8599 (tp)
REVERT: A 1059 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8214 (ttmm)
  outliers start: 5
  outliers final: 5
  residues processed: 41
  average time/residue: 0.1973
  time to fit residues: 13.4817
Evaluate side-chains
  43 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0010
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:   20.0000
   chunk 86 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12968  Z= 0.141
  Angle     :  0.494   8.833  18644  Z= 0.245
  Chirality :  0.031   0.196   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 23.002 177.409   4576
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.44 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.15 (0.29), residues: 924
  helix:  2.08 (0.25), residues: 457
  sheet:  0.33 (0.54), residues: 86
  loop : -0.78 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 581 
 HIS   0.008   0.001   HIS A 779 
 PHE   0.013   0.001   PHE A 331 
 TYR   0.010   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)
************************************************

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A  536 LEU cc_start: 0.8964 (tp) cc_final: 0.8623 (tp)
REVERT: A 1059 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8286 (ttmm)
  outliers start: 6
  outliers final: 5
  residues processed: 42
  average time/residue: 0.1911
  time to fit residues: 13.4730
Evaluate side-chains
  43 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 80 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0040
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12968  Z= 0.128
  Angle     :  0.489   8.869  18644  Z= 0.243
  Chirality :  0.030   0.197   2285
  Planarity :  0.004   0.031   1542
  Dihedral  : 22.968 177.303   4576
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.32 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.23 (0.29), residues: 924
  helix:  2.15 (0.25), residues: 458
  sheet:  0.38 (0.55), residues: 86
  loop : -0.76 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 581 
 HIS   0.009   0.001   HIS A 779 
 PHE   0.012   0.001   PHE A 331 
 TYR   0.010   0.001   TYR A 168 
 ARG   0.004   0.000   ARG A 132 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A 1054 MET cc_start: 0.7255 (ttm) cc_final: 0.7008 (ttm)
REVERT: A 1059 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8282 (ttmm)
  outliers start: 7
  outliers final: 5
  residues processed: 46
  average time/residue: 0.1991
  time to fit residues: 15.4079
Evaluate side-chains
  43 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 113 optimal weight:    0.1980
   chunk 104 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0270
   chunk 96 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    0.8040

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12968  Z= 0.138
  Angle     :  0.493   8.870  18644  Z= 0.244
  Chirality :  0.030   0.200   2285
  Planarity :  0.004   0.031   1542
  Dihedral  : 22.924 176.964   4576
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.44 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.27 (0.29), residues: 924
  helix:  2.20 (0.25), residues: 457
  sheet:  0.36 (0.52), residues: 96
  loop : -0.78 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 581 
 HIS   0.010   0.001   HIS A 779 
 PHE   0.013   0.001   PHE A 331 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.004   0.000   ARG A 885 

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 1.084 
Fit side-chains
REVERT: A  701 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7094 (m-30)
REVERT: A 1054 MET cc_start: 0.7261 (ttm) cc_final: 0.7015 (ttm)
REVERT: A 1059 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8277 (ttmm)
  outliers start: 7
  outliers final: 6
  residues processed: 43
  average time/residue: 0.2028
  time to fit residues: 14.6569
Evaluate side-chains
  44 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 25 optimal weight:   20.0000
   chunk 90 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0980
   chunk 93 optimal weight:    4.9990
   chunk 11 optimal weight:   30.0000
   chunk 16 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9980
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS
A1085 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.142852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.085731 restraints weight = 23130.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.23
r_work: 0.2974 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12968  Z= 0.333
  Angle     :  0.607   8.722  18644  Z= 0.303
  Chirality :  0.035   0.206   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 22.991 177.070   4576
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.44 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.82 (0.29), residues: 924
  helix:  1.80 (0.25), residues: 454
  sheet:  0.27 (0.51), residues: 96
  loop : -0.97 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 478 
 HIS   0.019   0.001   HIS A 779 
 PHE   0.026   0.002   PHE A 331 
 TYR   0.009   0.001   TYR A 462 
 ARG   0.005   0.001   ARG A 774 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2022.43 seconds
wall clock time: 40 minutes 50.03 seconds (2450.03 seconds total)