Starting phenix.real_space_refine
on Thu Mar 13 23:49:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c0f_45082/03_2025/9c0f_45082.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c0f_45082/03_2025/9c0f_45082.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c0f_45082/03_2025/9c0f_45082.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c0f_45082/03_2025/9c0f_45082.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c0f_45082/03_2025/9c0f_45082.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c0f_45082/03_2025/9c0f_45082.cif"
  }
  resolution = 3.6
  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=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P      70      5.49       5
     S      60      5.16       5
     C    5845      2.51       5
     N    1682      2.21       5
     O    1846      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9507
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 725
          Classifications: {'DNA': 35}
          Link IDs: {'rna3p': 34}
    Chain: "B"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 710
          Classifications: {'DNA': 35}
          Link IDs: {'rna3p': 34}
    Chain: "C"
      Number of atoms: 3883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 466, 3883
          Classifications: {'peptide': 466}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 450}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 4185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 4185
          Classifications: {'peptide': 504}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 484}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5131  SG  CYS C 550      61.208  48.152  33.030  1.00 65.65           S
  ATOM   5157  SG  CYS C 553      59.580  50.916  32.456  1.00 69.88           S
  ATOM   4997  SG  CYS C 534      52.649  39.523  29.596  1.00 66.98           S
  ATOM   5021  SG  CYS C 537      50.886  37.901  27.221  1.00 71.35           S
  ATOM   5222  SG  CYS C 562      54.572  38.672  26.797  1.00 70.35           S
  ATOM   9316  SG  CYS D 550      72.168  38.504  21.727  1.00104.21           S
  ATOM   9342  SG  CYS D 553      75.805  38.342  20.784  1.00108.94           S
  ATOM   9206  SG  CYS D 537      77.529  32.093  35.072  1.00114.33           S
  ATOM   9407  SG  CYS D 562      74.973  36.015  34.245  1.00105.23           S

  Time building chain proxies: 5.59, per 1000 atoms: 0.59
  Number of scatterers: 9507
  At special positions: 0
  Unit cell: (108.36, 134.16, 98.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      4     29.99
     S      60     16.00
     P      70     15.00
     O    1846      8.00
     N    1682      7.00
     C    5845      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: 2.43
  Conformation dependent library (CDL) restraints added in 878.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 601 "
        pdb="ZN    ZN C 601 " - pdb=" NE2 HIS C 567 "
        pdb="ZN    ZN C 601 " - pdb=" ND1 HIS C 516 "
        pdb="ZN    ZN C 601 " - pdb=" SG  CYS C 550 "
        pdb="ZN    ZN C 601 " - pdb=" SG  CYS C 553 "
      pdb="  ZN C 602 "
        pdb="ZN    ZN C 602 " - pdb=" ND1 HIS C 558 "
        pdb="ZN    ZN C 602 " - pdb=" SG  CYS C 562 "
        pdb="ZN    ZN C 602 " - pdb=" SG  CYS C 537 "
        pdb="ZN    ZN C 602 " - pdb=" SG  CYS C 534 "
      pdb="  ZN D 601 "
        pdb="ZN    ZN D 601 " - pdb=" ND1 HIS D 516 "
        pdb="ZN    ZN D 601 " - pdb=" NE2 HIS D 567 "
        pdb="ZN    ZN D 601 " - pdb=" SG  CYS D 550 "
        pdb="ZN    ZN D 601 " - pdb=" SG  CYS D 553 "
      pdb="  ZN D 602 "
        pdb="ZN    ZN D 602 " - pdb=" ND1 HIS D 558 "
        pdb="ZN    ZN D 602 " - pdb=" SG  CYS D 537 "
        pdb="ZN    ZN D 602 " - pdb=" SG  CYS D 562 "
      Number of angles added : 6


  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1856

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 9 sheets defined
      39.4% alpha, 11.0% beta
      33 base pairs and 55 stacking pairs defined.
    Time for finding SS restraints: 3.17
  Creating SS restraints...
    Processing helix  chain 'C' and resid 98 through 103
    Processing helix  chain 'C' and resid 107 through 125
    Processing helix  chain 'C' and resid 142 through 156
    Processing helix  chain 'C' and resid 163 through 169
      removed outlier: 4.063A  pdb=" N   TYR C 167 " --> pdb=" O   ARG C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 181
      removed outlier: 4.358A  pdb=" N   GLY C 180 " --> pdb=" O   THR C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 195
      removed outlier: 3.571A  pdb=" N   ALA C 194 " --> pdb=" O   GLN C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 227
      Proline residue:  C 222  - end of helix
      removed outlier: 3.526A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 297
    Processing helix  chain 'C' and resid 298 through 300
      No H-bonds generated for 'chain 'C' and resid 298 through 300'
    Processing helix  chain 'C' and resid 314 through 323
      removed outlier: 3.796A  pdb=" N   LYS C 323 " --> pdb=" O   GLU C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 346
    Processing helix  chain 'C' and resid 400 through 409
      removed outlier: 3.759A  pdb=" N   LYS C 407 " --> pdb=" O   ILE C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 410 through 415
    Processing helix  chain 'C' and resid 416 through 421
    Processing helix  chain 'C' and resid 430 through 455
    Processing helix  chain 'C' and resid 460 through 473
    Processing helix  chain 'C' and resid 505 through 510
      removed outlier: 4.345A  pdb=" N   LEU C 509 " --> pdb=" O   PRO C 506 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 534 through 539
      removed outlier: 3.747A  pdb=" N   VAL C 539 " --> pdb=" O   ARG C 535 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 569
      removed outlier: 4.007A  pdb=" N   LYS C 565 " --> pdb=" O   ALA C 561 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS C 567 " --> pdb=" O   PHE C 563 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 103
    Processing helix  chain 'D' and resid 107 through 125
    Processing helix  chain 'D' and resid 126 through 130
      removed outlier: 3.850A  pdb=" N   LYS D 130 " --> pdb=" O   ASN D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 156
      removed outlier: 3.814A  pdb=" N   LYS D 148 " --> pdb=" O   GLN D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 159
      No H-bonds generated for 'chain 'D' and resid 157 through 159'
    Processing helix  chain 'D' and resid 163 through 167
    Processing helix  chain 'D' and resid 171 through 175
      removed outlier: 3.935A  pdb=" N   GLU D 175 " --> pdb=" O   PRO D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 194
    Processing helix  chain 'D' and resid 213 through 228
      removed outlier: 3.641A  pdb=" N   TYR D 219 " --> pdb=" O   PRO D 215 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE D 220 " --> pdb=" O   VAL D 216 " (cutoff:3.500A)
      Proline residue:  D 222  - end of helix
      removed outlier: 4.395A  pdb=" N   TYR D 228 " --> pdb=" O   PHE D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 253
    Processing helix  chain 'D' and resid 296 through 300
    Processing helix  chain 'D' and resid 316 through 324
      removed outlier: 4.134A  pdb=" N   ALA D 320 " --> pdb=" O   ALA D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 339 through 343
    Processing helix  chain 'D' and resid 400 through 408
    Processing helix  chain 'D' and resid 413 through 418
      removed outlier: 3.500A  pdb=" N   GLN D 417 " --> pdb=" O   ASP D 413 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR D 418 " --> pdb=" O   ARG D 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 413 through 418'
    Processing helix  chain 'D' and resid 419 through 426
      removed outlier: 3.801A  pdb=" N   SER D 423 " --> pdb=" O   SER D 420 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   ILE D 424 " --> pdb=" O   TYR D 421 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 430 through 455
    Processing helix  chain 'D' and resid 460 through 473
    Processing helix  chain 'D' and resid 534 through 540
      removed outlier: 3.815A  pdb=" N   HIS D 540 " --> pdb=" O   VAL D 536 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 560 through 569
    Processing sheet with id=AA1, first strand: chain 'C' and resid 88 through 89
    Processing sheet with id=AA2, first strand: chain 'C' and resid 275 through 280
      removed outlier: 6.610A  pdb=" N   LEU C 267 " --> pdb=" O   CYS C 276 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   MET C 278 " --> pdb=" O   ARG C 265 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ARG C 265 " --> pdb=" O   MET C 278 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   ILE C 280 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   LEU C 263 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 382 through 386
    Processing sheet with id=AA4, first strand: chain 'C' and resid 518 through 520
      removed outlier: 4.151A  pdb=" N   TYR C 548 " --> pdb=" O   LEU C 557 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ILE C 555 " --> pdb=" O   CYS C 550 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 532 through 533
    Processing sheet with id=AA6, first strand: chain 'D' and resid 275 through 280
      removed outlier: 6.707A  pdb=" N   LEU D 267 " --> pdb=" O   CYS D 276 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   MET D 278 " --> pdb=" O   ARG D 265 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ARG D 265 " --> pdb=" O   MET D 278 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU D 234 " --> pdb=" O   TYR D 307 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR D 331 " --> pdb=" O   MET D 308 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 382 through 384
    Processing sheet with id=AA8, first strand: chain 'D' and resid 518 through 520
    Processing sheet with id=AA9, first strand: chain 'D' and resid 532 through 533

    278 hydrogen bonds defined for protein.
    747 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      84 hydrogen bonds
      168 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      55 stacking parallelities
  Total time for adding SS restraints: 2.96

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 1514
        1.30 -     1.44: 3413
        1.44 -     1.58: 4693
        1.58 -     1.72: 158
        1.72 -     1.86: 87
  Bond restraints: 9865
  Sorted by residual:
  bond pdb=" CB  HIS D 471 "
       pdb=" CG  HIS D 471 "
    ideal  model  delta    sigma   weight residual
    1.497  1.345  0.152 1.40e-02 5.10e+03 1.18e+02
  bond pdb=" CB  HIS C 231 "
       pdb=" CG  HIS C 231 "
    ideal  model  delta    sigma   weight residual
    1.497  1.370  0.127 1.40e-02 5.10e+03 8.20e+01
  bond pdb=" CB  PHE D 464 "
       pdb=" CG  PHE D 464 "
    ideal  model  delta    sigma   weight residual
    1.502  1.304  0.198 2.30e-02 1.89e+03 7.43e+01
  bond pdb=" CB  HIS D 558 "
       pdb=" CG  HIS D 558 "
    ideal  model  delta    sigma   weight residual
    1.497  1.383  0.114 1.40e-02 5.10e+03 6.58e+01
  bond pdb=" CB  PHE C 464 "
       pdb=" CG  PHE C 464 "
    ideal  model  delta    sigma   weight residual
    1.502  1.323  0.179 2.30e-02 1.89e+03 6.05e+01
  ... (remaining 9860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 11558
        2.52 -     5.03: 1730
        5.03 -     7.55: 255
        7.55 -    10.06: 39
       10.06 -    12.58: 9
  Bond angle restraints: 13591
  Sorted by residual:
  angle pdb=" N   VAL D 241 "
        pdb=" CA  VAL D 241 "
        pdb=" C   VAL D 241 "
      ideal   model   delta    sigma   weight residual
     109.02  117.60   -8.58 9.30e-01 1.16e+00 8.52e+01
  angle pdb=" C   LYS D 229 "
        pdb=" N   PRO D 230 "
        pdb=" CA  PRO D 230 "
      ideal   model   delta    sigma   weight residual
     120.52  129.30   -8.78 9.90e-01 1.02e+00 7.86e+01
  angle pdb=" C   THR C 176 "
        pdb=" N   PRO C 177 "
        pdb=" CA  PRO C 177 "
      ideal   model   delta    sigma   weight residual
     119.56  128.60   -9.04 1.02e+00 9.61e-01 7.86e+01
  angle pdb=" C   THR D 176 "
        pdb=" N   PRO D 177 "
        pdb=" CA  PRO D 177 "
      ideal   model   delta    sigma   weight residual
     119.56  128.06   -8.50 1.02e+00 9.61e-01 6.94e+01
  angle pdb=" N   ILE C 240 "
        pdb=" CA  ILE C 240 "
        pdb=" C   ILE C 240 "
      ideal   model   delta    sigma   weight residual
     108.11  119.48  -11.37 1.40e+00 5.10e-01 6.59e+01
  ... (remaining 13586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.31: 5400
       31.31 -    62.62: 355
       62.62 -    93.93: 8
       93.93 -   125.24: 0
      125.24 -   156.55: 1
  Dihedral angle restraints: 5764
    sinusoidal: 2892
      harmonic: 2872
  Sorted by residual:
  dihedral pdb=" C   PHE C 248 "
           pdb=" N   PHE C 248 "
           pdb=" CA  PHE C 248 "
           pdb=" CB  PHE C 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.79  -11.81     0      2.50e+00 1.60e-01 2.23e+01
  dihedral pdb=" C   ARG C 547 "
           pdb=" N   ARG C 547 "
           pdb=" CA  ARG C 547 "
           pdb=" CB  ARG C 547 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.87   11.27     0      2.50e+00 1.60e-01 2.03e+01
  dihedral pdb=" C   LYS C 541 "
           pdb=" N   LYS C 541 "
           pdb=" CA  LYS C 541 "
           pdb=" CB  LYS C 541 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.85   11.25     0      2.50e+00 1.60e-01 2.03e+01
  ... (remaining 5761 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 1036
       0.114 -    0.228: 350
       0.228 -    0.341: 58
       0.341 -    0.455: 7
       0.455 -    0.569: 4
  Chirality restraints: 1455
  Sorted by residual:
  chirality pdb=" CA  TYR D 260 "
            pdb=" N   TYR D 260 "
            pdb=" C   TYR D 260 "
            pdb=" CB  TYR D 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.09e+00
  chirality pdb=" CG  LEU C 288 "
            pdb=" CB  LEU C 288 "
            pdb=" CD1 LEU C 288 "
            pdb=" CD2 LEU C 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.09    0.50 2.00e-01 2.50e+01 6.24e+00
  chirality pdb=" CA  ARG C 547 "
            pdb=" N   ARG C 547 "
            pdb=" C   ARG C 547 "
            pdb=" CB  ARG C 547 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 5.98e+00
  ... (remaining 1452 not shown)

  Planarity restraints: 1470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA A  18 "    0.170 2.00e-02 2.50e+03   7.04e-02 1.36e+02
        pdb=" N9   DA A  18 "   -0.039 2.00e-02 2.50e+03
        pdb=" C8   DA A  18 "   -0.075 2.00e-02 2.50e+03
        pdb=" N7   DA A  18 "   -0.036 2.00e-02 2.50e+03
        pdb=" C5   DA A  18 "   -0.016 2.00e-02 2.50e+03
        pdb=" C6   DA A  18 "    0.024 2.00e-02 2.50e+03
        pdb=" N6   DA A  18 "    0.102 2.00e-02 2.50e+03
        pdb=" N1   DA A  18 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DA A  18 "   -0.035 2.00e-02 2.50e+03
        pdb=" N3   DA A  18 "   -0.052 2.00e-02 2.50e+03
        pdb=" C4   DA A  18 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA A  17 "    0.123 2.00e-02 2.50e+03   5.23e-02 7.51e+01
        pdb=" N9   DA A  17 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8   DA A  17 "   -0.049 2.00e-02 2.50e+03
        pdb=" N7   DA A  17 "   -0.037 2.00e-02 2.50e+03
        pdb=" C5   DA A  17 "   -0.015 2.00e-02 2.50e+03
        pdb=" C6   DA A  17 "    0.025 2.00e-02 2.50e+03
        pdb=" N6   DA A  17 "    0.069 2.00e-02 2.50e+03
        pdb=" N1   DA A  17 "    0.017 2.00e-02 2.50e+03
        pdb=" C2   DA A  17 "   -0.027 2.00e-02 2.50e+03
        pdb=" N3   DA A  17 "   -0.053 2.00e-02 2.50e+03
        pdb=" C4   DA A  17 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA B -24 "    0.100 2.00e-02 2.50e+03   4.83e-02 6.42e+01
        pdb=" N9   DA B -24 "    0.004 2.00e-02 2.50e+03
        pdb=" C8   DA B -24 "   -0.061 2.00e-02 2.50e+03
        pdb=" N7   DA B -24 "   -0.044 2.00e-02 2.50e+03
        pdb=" C5   DA B -24 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6   DA B -24 "    0.017 2.00e-02 2.50e+03
        pdb=" N6   DA B -24 "    0.083 2.00e-02 2.50e+03
        pdb=" N1   DA B -24 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2   DA B -24 "   -0.042 2.00e-02 2.50e+03
        pdb=" N3   DA B -24 "   -0.029 2.00e-02 2.50e+03
        pdb=" C4   DA B -24 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1467 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2943
        2.83 -     3.35: 8450
        3.35 -     3.87: 15941
        3.87 -     4.38: 19590
        4.38 -     4.90: 29074
  Nonbonded interactions: 75998
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 428 "
            pdb=" N   VAL C 429 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OG  SER C 423 "
            pdb=" N   ILE C 424 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OG  SER C 367 "
            pdb=" N   LYS C 368 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" N   LEU D 289 "
            pdb=" O   LEU D 289 "
     model   vdw
     2.387 2.496
  nonbonded pdb=" O5'  DG B -34 "
            pdb=" O4'  DG B -34 "
     model   vdw
     2.411 2.432
  ... (remaining 75993 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and (resid 78 through 284 or resid 288 through 332 or resid 341 throu \ 
gh 476 or resid 495 through 572 or resid 601 through 602))
}

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:             15.550
  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:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.150
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
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      :  0.026   0.198   9865  Z= 1.672
  Angle     :  1.890  12.581  13591  Z= 1.276
  Chirality :  0.114   0.569   1455
  Planarity :  0.011   0.085   1470
  Dihedral  : 16.991 156.551   3908
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.20 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  0.90 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.54 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.25), residues: 956
  helix: -0.91 (0.26), residues: 324
  sheet:  0.73 (0.49), residues: 95
  loop : -0.05 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.009   TRP C 243 
 HIS   0.015   0.003   HIS C 378 
 PHE   0.033   0.008   PHE D 563 
 TYR   0.085   0.012   TYR D 312 
 ARG   0.005   0.001   ARG D 533 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  382 MET cc_start: 0.7622 (ttt) cc_final: 0.7409 (ttt)
  outliers start: 3
  outliers final: 0
  residues processed: 129
  average time/residue: 0.3499
  time to fit residues: 58.1953
Evaluate side-chains
  59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.0870
   chunk 77 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    4.6166

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

Flipped N/Q/H residues before XYZ refinement:
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  73 HIS
D 305 HIS
D 317 ASN
** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.063269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.049942 restraints weight = 53180.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.051712 restraints weight = 28158.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.052894 restraints weight = 18711.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   9865  Z= 0.341
  Angle     :  0.804  10.070  13591  Z= 0.448
  Chirality :  0.047   0.386   1455
  Planarity :  0.005   0.042   1470
  Dihedral  : 21.654 157.721   1841
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.51 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  6.94 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.25), residues: 956
  helix:  0.34 (0.28), residues: 333
  sheet:  0.83 (0.57), residues: 73
  loop : -0.71 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C 138 
 HIS   0.007   0.002   HIS D  73 
 PHE   0.020   0.002   PHE C 149 
 TYR   0.041   0.002   TYR C 422 
 ARG   0.007   0.001   ARG D 434 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  262 ILE cc_start: 0.8051 (mp) cc_final: 0.7573 (mm)
REVERT: D  231 HIS cc_start: 0.5699 (m170) cc_final: 0.5455 (m170)
REVERT: D  382 MET cc_start: 0.9622 (mmm) cc_final: 0.9138 (tpp)
REVERT: D  513 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8581 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 73
  average time/residue: 0.2877
  time to fit residues: 28.8923
Evaluate side-chains
  68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  241 VAL
Chi-restraints excluded: chain C residue  276 CYS
Chi-restraints excluded: chain C residue  280 ILE
Chi-restraints excluded: chain C residue  326 PHE
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  536 VAL
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain D residue  440 ILE
Chi-restraints excluded: chain D residue  513 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0270
   chunk 39 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   overall best weight:    0.8842

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

Flipped N/Q/H residues before XYZ refinement:
C  87 GLN
C 196 HIS
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 317 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.065957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.053016 restraints weight = 57054.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.054788 restraints weight = 31396.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.055948 restraints weight = 21206.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9865  Z= 0.177
  Angle     :  0.643   9.208  13591  Z= 0.353
  Chirality :  0.041   0.170   1455
  Planarity :  0.004   0.033   1470
  Dihedral  : 21.733 168.537   1841
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.45 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.95 %
    Favored  : 91.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.01 (0.26), residues: 956
  helix:  0.92 (0.29), residues: 331
  sheet:  0.75 (0.54), residues: 83
  loop : -0.68 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 138 
 HIS   0.004   0.001   HIS C 231 
 PHE   0.013   0.001   PHE C 445 
 TYR   0.026   0.002   TYR C 312 
 ARG   0.005   0.000   ARG D 434 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  262 ILE cc_start: 0.7960 (mp) cc_final: 0.7612 (mm)
REVERT: C  496 MET cc_start: 0.7904 (ttp) cc_final: 0.7668 (ttp)
REVERT: D  382 MET cc_start: 0.9681 (mmm) cc_final: 0.9168 (mmm)
REVERT: D  496 MET cc_start: 0.7660 (tmm) cc_final: 0.6925 (tmm)
REVERT: D  549 MET cc_start: 0.8595 (ttp) cc_final: 0.7545 (tmm)
  outliers start: 9
  outliers final: 4
  residues processed: 67
  average time/residue: 0.2348
  time to fit residues: 22.2856
Evaluate side-chains
  59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  459 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 86 optimal weight:    0.4980
   chunk 18 optimal weight:   20.0000
   chunk 67 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0270
   overall best weight:    3.9044

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

Flipped N/Q/H residues before XYZ refinement:
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.062262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.048903 restraints weight = 54153.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.050573 restraints weight = 30186.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.051694 restraints weight = 20662.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9865  Z= 0.262
  Angle     :  0.638   9.108  13591  Z= 0.350
  Chirality :  0.041   0.160   1455
  Planarity :  0.004   0.032   1470
  Dihedral  : 21.635 166.611   1841
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.18 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  7.50 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 956
  helix:  1.16 (0.30), residues: 332
  sheet:  0.57 (0.53), residues: 83
  loop : -0.82 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP D 138 
 HIS   0.005   0.001   HIS C 231 
 PHE   0.017   0.002   PHE C 149 
 TYR   0.028   0.002   TYR C 422 
 ARG   0.007   0.000   ARG D 120 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  262 ILE cc_start: 0.7903 (mp) cc_final: 0.7669 (mm)
REVERT: C  513 MET cc_start: 0.8387 (mpp) cc_final: 0.8166 (mmt)
REVERT: D  183 MET cc_start: 0.8183 (mtt) cc_final: 0.7842 (mtt)
REVERT: D  382 MET cc_start: 0.9651 (mmm) cc_final: 0.9069 (mmm)
REVERT: D  496 MET cc_start: 0.7634 (tmm) cc_final: 0.7140 (tmm)
  outliers start: 17
  outliers final: 12
  residues processed: 66
  average time/residue: 0.3130
  time to fit residues: 29.7383
Evaluate side-chains
  66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain C residue  326 PHE
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain C residue  530 ILE
Chi-restraints excluded: chain C residue  536 VAL
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  413 ASP
Chi-restraints excluded: chain D residue  459 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 92 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   chunk 97 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0020
   chunk 67 optimal weight:    0.0370
   overall best weight:    3.2072

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

Flipped N/Q/H residues before XYZ refinement:
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.061844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.048416 restraints weight = 54278.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.050072 restraints weight = 30322.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.051178 restraints weight = 20820.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9865  Z= 0.218
  Angle     :  0.605  10.384  13591  Z= 0.330
  Chirality :  0.040   0.148   1455
  Planarity :  0.003   0.033   1470
  Dihedral  : 21.511 167.434   1841
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.08 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.18 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 956
  helix:  1.22 (0.30), residues: 337
  sheet:  0.21 (0.53), residues: 88
  loop : -0.82 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 138 
 HIS   0.005   0.001   HIS C 231 
 PHE   0.015   0.001   PHE C 149 
 TYR   0.027   0.002   TYR C 422 
 ARG   0.006   0.000   ARG D 356 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  289 LEU cc_start: 0.9025 (tt) cc_final: 0.8666 (tp)
REVERT: C  513 MET cc_start: 0.8548 (mpp) cc_final: 0.8315 (mmt)
REVERT: D  130 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8753 (ptpp)
REVERT: D  183 MET cc_start: 0.8288 (mtt) cc_final: 0.7990 (mtt)
REVERT: D  382 MET cc_start: 0.9673 (mmm) cc_final: 0.9078 (mmm)
REVERT: D  386 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7942 (tt0)
REVERT: D  496 MET cc_start: 0.7649 (tmm) cc_final: 0.7402 (tmm)
REVERT: D  549 MET cc_start: 0.8566 (ttp) cc_final: 0.7634 (tmm)
  outliers start: 13
  outliers final: 9
  residues processed: 68
  average time/residue: 0.3401
  time to fit residues: 32.8330
Evaluate side-chains
  68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  276 CYS
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain C residue  530 ILE
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  386 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0470
   chunk 69 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0020
   chunk 80 optimal weight:    0.5980
   chunk 53 optimal weight:    9.9990
   chunk 96 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    1.3290

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

Flipped N/Q/H residues before XYZ refinement:
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.062894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.049403 restraints weight = 54242.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.051127 restraints weight = 29707.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.052280 restraints weight = 20140.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.4583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9865  Z= 0.154
  Angle     :  0.579  10.029  13591  Z= 0.311
  Chirality :  0.039   0.143   1455
  Planarity :  0.003   0.043   1470
  Dihedral  : 21.402 166.275   1841
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.50 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.41 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.27), residues: 956
  helix:  1.54 (0.30), residues: 332
  sheet:  0.82 (0.58), residues: 70
  loop : -0.77 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 138 
 HIS   0.004   0.001   HIS C 231 
 PHE   0.009   0.001   PHE C 445 
 TYR   0.033   0.001   TYR C 422 
 ARG   0.021   0.000   ARG C 514 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  262 ILE cc_start: 0.7778 (mp) cc_final: 0.7029 (tp)
REVERT: C  278 MET cc_start: 0.8386 (ttp) cc_final: 0.7549 (tpp)
REVERT: C  437 MET cc_start: 0.7869 (tpt) cc_final: 0.7492 (ttp)
REVERT: C  513 MET cc_start: 0.8616 (mpp) cc_final: 0.8364 (mmt)
REVERT: D  183 MET cc_start: 0.8205 (mtt) cc_final: 0.7898 (mtt)
REVERT: D  382 MET cc_start: 0.9692 (mmm) cc_final: 0.9052 (mmm)
REVERT: D  409 MET cc_start: 0.7871 (tpp) cc_final: 0.7627 (mmp)
REVERT: D  549 MET cc_start: 0.8524 (ttp) cc_final: 0.7626 (tmm)
  outliers start: 11
  outliers final: 9
  residues processed: 67
  average time/residue: 0.2226
  time to fit residues: 22.0229
Evaluate side-chains
  65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  276 CYS
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain C residue  530 ILE
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  360 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 36 optimal weight:    0.0040
   chunk 22 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 98 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 95 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.2394

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

Flipped N/Q/H residues before XYZ refinement:
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.063124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.049617 restraints weight = 54374.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.051351 restraints weight = 29728.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.052508 restraints weight = 20072.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9865  Z= 0.145
  Angle     :  0.559  11.923  13591  Z= 0.299
  Chirality :  0.039   0.150   1455
  Planarity :  0.003   0.039   1470
  Dihedral  : 21.388 164.828   1841
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.39 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.85 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.37 (0.28), residues: 956
  helix:  1.62 (0.30), residues: 336
  sheet:  0.40 (0.57), residues: 83
  loop : -0.68 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 138 
 HIS   0.004   0.001   HIS C 408 
 PHE   0.008   0.001   PHE C 326 
 TYR   0.025   0.001   TYR C 422 
 ARG   0.009   0.000   ARG C 514 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  262 ILE cc_start: 0.7787 (mp) cc_final: 0.7513 (mm)
REVERT: C  278 MET cc_start: 0.8358 (ttp) cc_final: 0.7562 (tpp)
REVERT: D  183 MET cc_start: 0.8139 (mtt) cc_final: 0.7832 (mtt)
REVERT: D  292 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8021 (pt)
REVERT: D  308 MET cc_start: 0.8234 (ptm) cc_final: 0.7896 (ptp)
REVERT: D  382 MET cc_start: 0.9692 (mmm) cc_final: 0.9051 (mmm)
REVERT: D  409 MET cc_start: 0.7734 (tpp) cc_final: 0.7502 (mmp)
REVERT: D  549 MET cc_start: 0.8504 (ttp) cc_final: 0.7501 (tmm)
  outliers start: 10
  outliers final: 7
  residues processed: 66
  average time/residue: 0.2329
  time to fit residues: 22.0096
Evaluate side-chains
  63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  276 CYS
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain C residue  530 ILE
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  360 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 80 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.060016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.046595 restraints weight = 55196.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.048161 restraints weight = 31143.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.049203 restraints weight = 21446.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.4990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9865  Z= 0.332
  Angle     :  0.667  11.038  13591  Z= 0.363
  Chirality :  0.043   0.184   1455
  Planarity :  0.004   0.040   1470
  Dihedral  : 21.485 158.411   1841
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.02 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  9.63 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.27), residues: 956
  helix:  1.24 (0.30), residues: 341
  sheet:  0.51 (0.59), residues: 80
  loop : -0.96 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 431 
 HIS   0.006   0.001   HIS C 231 
 PHE   0.021   0.002   PHE C 149 
 TYR   0.034   0.002   TYR C 422 
 ARG   0.014   0.001   ARG C 514 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  278 MET cc_start: 0.8381 (ttp) cc_final: 0.7670 (tpp)
REVERT: C  356 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7143 (mtt90)
REVERT: D  130 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8314 (ptpp)
REVERT: D  183 MET cc_start: 0.8442 (mtt) cc_final: 0.8209 (mtt)
REVERT: D  382 MET cc_start: 0.9638 (mmm) cc_final: 0.9028 (mmm)
  outliers start: 16
  outliers final: 12
  residues processed: 67
  average time/residue: 0.2486
  time to fit residues: 23.2638
Evaluate side-chains
  68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  276 CYS
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain C residue  326 PHE
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  413 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0770
   chunk 98 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    1.3942

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

Flipped N/Q/H residues before XYZ refinement:
C 313 ASN
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.061975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.048474 restraints weight = 54202.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.050140 restraints weight = 30233.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.051263 restraints weight = 20654.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9865  Z= 0.168
  Angle     :  0.628  12.198  13591  Z= 0.332
  Chirality :  0.040   0.276   1455
  Planarity :  0.004   0.093   1470
  Dihedral  : 21.387 160.145   1841
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.77 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.75 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.28), residues: 956
  helix:  1.43 (0.30), residues: 341
  sheet:  0.92 (0.65), residues: 70
  loop : -0.86 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 138 
 HIS   0.004   0.001   HIS C 231 
 PHE   0.010   0.001   PHE D 249 
 TYR   0.022   0.001   TYR C 422 
 ARG   0.021   0.000   ARG D 287 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  181 LYS cc_start: 0.9226 (mttt) cc_final: 0.8924 (mtpt)
REVERT: C  278 MET cc_start: 0.8423 (ttp) cc_final: 0.7629 (tpp)
REVERT: C  356 ARG cc_start: 0.7314 (mtm180) cc_final: 0.6907 (mtt180)
REVERT: C  496 MET cc_start: 0.7746 (ttp) cc_final: 0.7477 (ttp)
REVERT: D  130 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8398 (ptpp)
REVERT: D  183 MET cc_start: 0.8268 (mtt) cc_final: 0.8026 (mtt)
REVERT: D  382 MET cc_start: 0.9660 (mmm) cc_final: 0.9069 (mmm)
REVERT: D  549 MET cc_start: 0.8539 (ttp) cc_final: 0.7506 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 66
  average time/residue: 0.2482
  time to fit residues: 23.1034
Evaluate side-chains
  64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain D residue  130 LYS
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  360 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 55 optimal weight:   30.0000
   chunk 50 optimal weight:    0.2980
   chunk 81 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0050
   overall best weight:    2.0600

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

Flipped N/Q/H residues before XYZ refinement:
C 313 ASN
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.061848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.048393 restraints weight = 55166.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.050054 restraints weight = 30576.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.051187 restraints weight = 20799.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.5301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9865  Z= 0.185
  Angle     :  0.625  12.128  13591  Z= 0.329
  Chirality :  0.039   0.205   1455
  Planarity :  0.004   0.069   1470
  Dihedral  : 21.318 159.239   1841
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.39 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.86 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.28), residues: 956
  helix:  1.50 (0.31), residues: 341
  sheet:  0.99 (0.65), residues: 70
  loop : -0.91 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 138 
 HIS   0.004   0.001   HIS C 231 
 PHE   0.010   0.001   PHE C 342 
 TYR   0.026   0.001   TYR D 260 
 ARG   0.015   0.000   ARG C 514 

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  181 LYS cc_start: 0.9263 (mttt) cc_final: 0.9033 (mtpt)
REVERT: C  278 MET cc_start: 0.8364 (ttp) cc_final: 0.7588 (tpp)
REVERT: C  356 ARG cc_start: 0.7228 (mtm180) cc_final: 0.6828 (mtt180)
REVERT: C  496 MET cc_start: 0.7739 (ttp) cc_final: 0.7524 (ttp)
REVERT: D  183 MET cc_start: 0.8304 (mtt) cc_final: 0.8043 (mtt)
REVERT: D  382 MET cc_start: 0.9669 (mmm) cc_final: 0.9047 (mmm)
REVERT: D  409 MET cc_start: 0.7479 (mmp) cc_final: 0.7234 (mmp)
REVERT: D  549 MET cc_start: 0.8564 (ttp) cc_final: 0.7522 (tmm)
  outliers start: 9
  outliers final: 7
  residues processed: 63
  average time/residue: 0.2391
  time to fit residues: 21.4725
Evaluate side-chains
  64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  248 PHE
Chi-restraints excluded: chain C residue  312 TYR
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  360 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.061096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.047717 restraints weight = 55110.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.049344 restraints weight = 30893.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.050392 restraints weight = 21123.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.5336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9865  Z= 0.241
  Angle     :  0.646  12.447  13591  Z= 0.342
  Chirality :  0.040   0.202   1455
  Planarity :  0.004   0.066   1470
  Dihedral  : 21.334 158.260   1841
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.33 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.97 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.28), residues: 956
  helix:  1.41 (0.30), residues: 342
  sheet:  0.86 (0.65), residues: 70
  loop : -0.97 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 138 
 HIS   0.005   0.001   HIS C 231 
 PHE   0.014   0.001   PHE C 149 
 TYR   0.022   0.002   TYR C 422 
 ARG   0.013   0.000   ARG D 287 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3615.52 seconds
wall clock time: 65 minutes 32.34 seconds (3932.34 seconds total)